From 9b52008c1aa8ef5fe1b23735f23d6109d5d7da84 Mon Sep 17 00:00:00 2001
From: "Aidan Cunniffe (windows machine)" <acunniffe@gmail.com>
Date: Sat, 8 Nov 2025 09:38:16 -0500
Subject: [PATCH 01/19] fixes

---
 scripts/dev-symlinks.sh                    |  0
 src/authorship/post_commit.rs              |  1 +
 src/authorship/rebase_authorship.rs        |  7 ++++++
 src/commands/checkpoint.rs                 | 25 +++++++++++++++++++---
 src/commands/git_ai_handlers.rs            |  3 +++
 tests/amend.rs                             |  1 -
 tests/git-compat/run.py                    |  0
 tests/github/scripts/cleanup-test-repos.sh |  0
 tests/github/scripts/run-github-tests.sh   |  0
 tests/repos/test_file.rs                   |  4 +++-
 tests/repos/test_repo.rs                   |  2 +-
 11 files changed, 37 insertions(+), 6 deletions(-)
 mode change 100755 => 100644 scripts/dev-symlinks.sh
 mode change 100755 => 100644 tests/git-compat/run.py
 mode change 100755 => 100644 tests/github/scripts/cleanup-test-repos.sh
 mode change 100755 => 100644 tests/github/scripts/run-github-tests.sh

diff --git a/scripts/dev-symlinks.sh b/scripts/dev-symlinks.sh
old mode 100755
new mode 100644
diff --git a/src/authorship/post_commit.rs b/src/authorship/post_commit.rs
index a11b5036..bc121c4f 100644
--- a/src/authorship/post_commit.rs
+++ b/src/authorship/post_commit.rs
@@ -54,6 +54,7 @@ pub fn post_commit(
         .flat_map(|cp| cp.entries.iter().map(|e| e.file.clone()))
         .collect();
 
+
     // Split VirtualAttributions into committed (authorship log) and uncommitted (INITIAL)
     let (mut authorship_log, initial_attributions) = working_va
         .to_authorship_log_and_initial_working_log(
diff --git a/src/authorship/rebase_authorship.rs b/src/authorship/rebase_authorship.rs
index 68226008..e4ae3364 100644
--- a/src/authorship/rebase_authorship.rs
+++ b/src/authorship/rebase_authorship.rs
@@ -706,10 +706,14 @@ pub fn rewrite_authorship_after_commit_amend(
     let changed_files = repo.list_commit_files(amended_commit, None)?;
     let mut pathspecs: HashSet<String> = changed_files.into_iter().collect();
 
+    // println!("changed_files: {:?}", changed_files);
+
     let working_log = repo.storage.working_log_for_base_commit(original_commit);
     let touched_files = working_log.all_touched_files()?;
     pathspecs.extend(touched_files);
 
+    println!("pathspecs: {:?}", pathspecs);
+
     // Check if original commit has an authorship log with prompts
     let has_existing_log = get_reference_as_authorship_log_v3(repo, original_commit).is_ok();
     let has_existing_prompts = if has_existing_log {
@@ -756,6 +760,9 @@ pub fn rewrite_authorship_after_commit_amend(
             Some(&pathspecs_set),
         )?;
 
+
+    println!("authorship_log: {:?}", authorship_log);
+    println!("initial_attributions: {:?}", initial_attributions);
     // Update base commit SHA
     authorship_log.metadata.base_commit_sha = amended_commit.to_string();
 
diff --git a/src/commands/checkpoint.rs b/src/commands/checkpoint.rs
index eb065ef5..4c9080d3 100644
--- a/src/commands/checkpoint.rs
+++ b/src/commands/checkpoint.rs
@@ -24,6 +24,8 @@ pub fn run(
     agent_run_result: Option<AgentRunResult>,
     is_pre_commit: bool,
 ) -> Result<(usize, usize, usize), GitAiError> {
+
+
     // Robustly handle zero-commit repos
     let base_commit = match repo.head() {
         Ok(head) => match head.target() {
@@ -73,13 +75,24 @@ pub fn run(
 
         paths.and_then(|p| {
             let repo_workdir = repo.workdir().ok()?;
+            
+            // CRITICAL FIX: Canonicalize repo_workdir for consistent path comparison on Windows
+            // On Windows, canonicalize() returns paths with \\?\ UNC prefix, so both paths
+            // must be canonicalized for starts_with() to work correctly
+            let canonical_repo_workdir = repo_workdir.canonicalize().ok()?;
+            
             let filtered: Vec<String> = p
                 .iter()
                 .filter_map(|path| {
                     // Check if path is absolute and outside repo
                     if std::path::Path::new(path).is_absolute() {
-                        // For absolute paths, check if they start with repo_workdir
-                        if !std::path::Path::new(path).starts_with(&repo_workdir) {
+                        // For absolute paths, canonicalize and compare with canonical_repo_workdir
+                        if let Ok(canonical_path) = std::path::Path::new(path).canonicalize() {
+                            if !canonical_path.starts_with(&canonical_repo_workdir) {
+                                return None;
+                            }
+                        } else if !std::path::Path::new(path).starts_with(&repo_workdir) {
+                            // Fallback if canonicalize fails
                             return None;
                         }
                     } else {
@@ -87,7 +100,8 @@ pub fn run(
                         let joined = repo_workdir.join(path);
                         // Try to canonicalize to resolve .. and . components
                         if let Ok(canonical) = joined.canonicalize() {
-                            if !canonical.starts_with(&repo_workdir) {
+                            // Compare canonical paths (both have \\?\ prefix on Windows)
+                            if !canonical.starts_with(&canonical_repo_workdir) {
                                 return None;
                             }
                         } else {
@@ -106,6 +120,7 @@ pub fn run(
                                     acc
                                 },
                             );
+                            // For the fallback, compare against the original repo_workdir
                             if !normalized_joined.starts_with(&repo_workdir) {
                                 return None;
                             }
@@ -124,6 +139,8 @@ pub fn run(
         })
     });
 
+
+    println!("pathspec_filter: {:?}", pathspec_filter);
     let files = get_all_tracked_files(
         repo,
         &base_commit,
@@ -132,6 +149,8 @@ pub fn run(
         is_pre_commit,
     )?;
 
+    println!("files: {:?}", files);
+
     let mut checkpoints = if reset {
         // If reset flag is set, start with an empty working log
         working_log.reset_working_log()?;
diff --git a/src/commands/git_ai_handlers.rs b/src/commands/git_ai_handlers.rs
index a83b6ca4..b083ae21 100644
--- a/src/commands/git_ai_handlers.rs
+++ b/src/commands/git_ai_handlers.rs
@@ -326,6 +326,9 @@ fn handle_checkpoint(args: &[String]) {
         .map(|r| r.checkpoint_kind)
         .unwrap_or(CheckpointKind::Human);
 
+    println!("checkpoint_kind: {:?}", checkpoint_kind);
+    println!("files for mock_ai: {:?}", get_all_files_for_mock_ai(&final_working_dir));
+
     if CheckpointKind::Human == checkpoint_kind && agent_run_result.is_none() {
         println!(
             "get_all_files_for_mock_ai HUMAN Checkpoints: {:?}",
diff --git a/tests/amend.rs b/tests/amend.rs
index 429968ec..d7350add 100644
--- a/tests/amend.rs
+++ b/tests/amend.rs
@@ -24,7 +24,6 @@ fn test_amend_add_lines_at_top() {
     );
 
     // Amend the commit WITHOUT staging the AI lines
-    // repo.git(&["add", "-A"]).unwrap();
     repo.git(&["commit", "--amend", "-m", "Initial commit (amended)"])
         .unwrap();
 
diff --git a/tests/git-compat/run.py b/tests/git-compat/run.py
old mode 100755
new mode 100644
diff --git a/tests/github/scripts/cleanup-test-repos.sh b/tests/github/scripts/cleanup-test-repos.sh
old mode 100755
new mode 100644
diff --git a/tests/github/scripts/run-github-tests.sh b/tests/github/scripts/run-github-tests.sh
old mode 100755
new mode 100644
diff --git a/tests/repos/test_file.rs b/tests/repos/test_file.rs
index 01dd4981..f0de88de 100644
--- a/tests/repos/test_file.rs
+++ b/tests/repos/test_file.rs
@@ -728,7 +728,9 @@ impl<'a> TestFile<'a> {
         let contents = self.contents();
         fs::write(&self.file_path, contents).unwrap();
         let _ = if author_type == &AuthorType::Ai {
-            self.repo.git_ai(&["checkpoint", "mock_ai"])
+            let a = self.repo.git_ai(&["checkpoint", "mock_ai"]);
+            println!("checkpoint result: {:?}", a);
+            a
         } else {
             self.repo.git_ai(&["checkpoint"])
         };
diff --git a/tests/repos/test_repo.rs b/tests/repos/test_repo.rs
index 3395fb1a..e0cc0560 100644
--- a/tests/repos/test_repo.rs
+++ b/tests/repos/test_repo.rs
@@ -224,7 +224,7 @@ impl TestRepo {
 
 impl Drop for TestRepo {
     fn drop(&mut self) {
-        fs::remove_dir_all(self.path.clone()).expect("failed to remove test repo");
+        // fs::remove_dir_all(self.path.clone()).expect("failed to remove test repo");
     }
 }
 

From fd4321d553e6377c3848a098b4c83dcddff08685 Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Sat, 8 Nov 2025 09:51:53 -0500
Subject: [PATCH 02/19] add canonical working dir

---
 src/commands/checkpoint.rs | 58 ++++++++------------------------------
 src/git/repository.rs      | 40 +++++++++++++++++++++++++-
 2 files changed, 51 insertions(+), 47 deletions(-)

diff --git a/src/commands/checkpoint.rs b/src/commands/checkpoint.rs
index 4c9080d3..40ab17de 100644
--- a/src/commands/checkpoint.rs
+++ b/src/commands/checkpoint.rs
@@ -76,57 +76,23 @@ pub fn run(
         paths.and_then(|p| {
             let repo_workdir = repo.workdir().ok()?;
             
-            // CRITICAL FIX: Canonicalize repo_workdir for consistent path comparison on Windows
-            // On Windows, canonicalize() returns paths with \\?\ UNC prefix, so both paths
-            // must be canonicalized for starts_with() to work correctly
-            let canonical_repo_workdir = repo_workdir.canonicalize().ok()?;
-            
             let filtered: Vec<String> = p
                 .iter()
                 .filter_map(|path| {
-                    // Check if path is absolute and outside repo
-                    if std::path::Path::new(path).is_absolute() {
-                        // For absolute paths, canonicalize and compare with canonical_repo_workdir
-                        if let Ok(canonical_path) = std::path::Path::new(path).canonicalize() {
-                            if !canonical_path.starts_with(&canonical_repo_workdir) {
-                                return None;
-                            }
-                        } else if !std::path::Path::new(path).starts_with(&repo_workdir) {
-                            // Fallback if canonicalize fails
-                            return None;
-                        }
+                    let path_buf = if std::path::Path::new(path).is_absolute() {
+                        // Absolute path - check directly
+                        std::path::PathBuf::from(path)
                     } else {
-                        // For relative paths, join with workdir and canonicalize to check
-                        let joined = repo_workdir.join(path);
-                        // Try to canonicalize to resolve .. and . components
-                        if let Ok(canonical) = joined.canonicalize() {
-                            // Compare canonical paths (both have \\?\ prefix on Windows)
-                            if !canonical.starts_with(&canonical_repo_workdir) {
-                                return None;
-                            }
-                        } else {
-                            // If we can't canonicalize (file doesn't exist), check the joined path
-                            // Convert both to canonical form if possible, otherwise use as-is
-                            let normalized_joined = joined.components().fold(
-                                std::path::PathBuf::new(),
-                                |mut acc, component| {
-                                    match component {
-                                        std::path::Component::ParentDir => {
-                                            acc.pop();
-                                        }
-                                        std::path::Component::CurDir => {}
-                                        _ => acc.push(component),
-                                    }
-                                    acc
-                                },
-                            );
-                            // For the fallback, compare against the original repo_workdir
-                            if !normalized_joined.starts_with(&repo_workdir) {
-                                return None;
-                            }
-                        }
+                        // Relative path - join with workdir
+                        repo_workdir.join(path)
+                    };
+                    
+                    // Use centralized path comparison (handles Windows canonical paths correctly)
+                    if repo.path_is_in_workdir(&path_buf) {
+                        Some(path.clone())
+                    } else {
+                        None
                     }
-                    Some(path.clone())
                 })
                 .collect();
 
diff --git a/src/git/repository.rs b/src/git/repository.rs
index 69c37f80..7fcfe38e 100644
--- a/src/git/repository.rs
+++ b/src/git/repository.rs
@@ -790,6 +790,9 @@ pub struct Repository {
     pub pre_command_base_commit: Option<String>,
     pub pre_command_refname: Option<String>,
     workdir: PathBuf,
+    /// Canonical (absolute, resolved) version of workdir for reliable path comparisons
+    /// On Windows, this uses the \\?\ UNC prefix format
+    canonical_workdir: PathBuf,
 }
 
 impl Repository {
@@ -902,6 +905,31 @@ impl Repository {
         Ok(self.workdir.clone())
     }
 
+    /// Check if a path is within the repository's working directory
+    /// Uses canonical path comparison for reliability on Windows
+    pub fn path_is_in_workdir(&self, path: &Path) -> bool {
+        // Try canonical comparison first (most reliable, especially on Windows)
+        if let Ok(canonical_path) = path.canonicalize() {
+            return canonical_path.starts_with(&self.canonical_workdir);
+        }
+        
+        // Fallback for paths that don't exist yet: normalize by resolving .. and .
+        let normalized = path.components().fold(
+            std::path::PathBuf::new(),
+            |mut acc, component| {
+                match component {
+                    std::path::Component::ParentDir => {
+                        acc.pop();
+                    }
+                    std::path::Component::CurDir => {}
+                    _ => acc.push(component),
+                }
+                acc
+            },
+        );
+        normalized.starts_with(&self.workdir)
+    }
+
     // List all remotes for a given repository
     pub fn remotes(&self) -> Result<Vec<String>, GitAiError> {
         let mut args = self.global_args_for_exec();
@@ -1696,7 +1724,16 @@ pub fn find_repository(global_args: &Vec<String>) -> Result<Repository, GitAiErr
         )));
     }
 
-    // TODO Consider if we should canonicalize the paths (sometimes git will return symlinked paths)
+    // Canonicalize workdir for reliable path comparisons (especially on Windows)
+    // On Windows, canonical paths use the \\?\ UNC prefix, which makes path.starts_with()
+    // comparisons work correctly. We store both regular and canonical versions.
+    let canonical_workdir = workdir.canonicalize().map_err(|e| {
+        GitAiError::Generic(format!(
+            "Failed to canonicalize working directory {}: {}",
+            workdir.display(),
+            e
+        ))
+    })?;
 
     Ok(Repository {
         global_args: global_args.clone(),
@@ -1705,6 +1742,7 @@ pub fn find_repository(global_args: &Vec<String>) -> Result<Repository, GitAiErr
         pre_command_base_commit: None,
         pre_command_refname: None,
         workdir,
+        canonical_workdir,
     })
 }
 

From 1006efbf661edcfc8dd410907010ee6ec4f7122a Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Sat, 8 Nov 2025 10:36:15 -0500
Subject: [PATCH 03/19] windows fix

---
 src/commands/checkpoint.rs | 53 ++++++++++++++++++++++++++++----------
 src/git/repository.rs      |  6 +++++
 src/utils.rs               | 25 ++++++++++++++++++
 tests/ai_tab.rs            | 38 ++++++++++++++++++++-------
 tests/repos/test_repo.rs   |  4 +++
 5 files changed, 104 insertions(+), 22 deletions(-)

diff --git a/src/commands/checkpoint.rs b/src/commands/checkpoint.rs
index 40ab17de..5614968a 100644
--- a/src/commands/checkpoint.rs
+++ b/src/commands/checkpoint.rs
@@ -7,7 +7,7 @@ use crate::error::GitAiError;
 use crate::git::repo_storage::{PersistedWorkingLog, RepoStorage};
 use crate::git::repository::Repository;
 use crate::git::status::{EntryKind, StatusCode};
-use crate::utils::debug_log;
+use crate::utils::{debug_log, normalize_to_posix};
 use sha2::{Digest, Sha256};
 use similar::{ChangeTag, TextDiff};
 use std::collections::{HashMap, HashSet};
@@ -89,7 +89,26 @@ pub fn run(
                     
                     // Use centralized path comparison (handles Windows canonical paths correctly)
                     if repo.path_is_in_workdir(&path_buf) {
-                        Some(path.clone())
+                        // Convert to relative path for git operations
+                        if std::path::Path::new(path).is_absolute() {
+                            if let Ok(relative) = path_buf.strip_prefix(&repo_workdir) {
+                                // Normalize path separators to forward slashes for git
+                                Some(normalize_to_posix(&relative.to_string_lossy()))
+                            } else {
+                                // Fallback: try with canonical paths
+                                let canonical_workdir = repo_workdir.canonicalize().ok()?;
+                                let canonical_path = path_buf.canonicalize().ok()?;
+                                if let Ok(relative) = canonical_path.strip_prefix(&canonical_workdir) {
+                                    // Normalize path separators to forward slashes for git
+                                    Some(normalize_to_posix(&relative.to_string_lossy()))
+                                } else {
+                                    None
+                                }
+                            }
+                        } else {
+                            // Normalize path separators to forward slashes for git
+                            Some(normalize_to_posix(path))
+                        }
                     } else {
                         None
                     }
@@ -357,18 +376,22 @@ fn get_all_tracked_files(
         .unwrap_or_default();
 
     for file in working_log.read_initial_attributions().files.keys() {
-        if is_text_file(working_log, &file) {
-            files.insert(file.clone());
+        // Normalize path separators to forward slashes
+        let normalized_path = normalize_to_posix(file);
+        if is_text_file(working_log, &normalized_path) {
+            files.insert(normalized_path);
         }
     }
 
     if let Ok(working_log_data) = working_log.read_all_checkpoints() {
         for checkpoint in &working_log_data {
             for entry in &checkpoint.entries {
-                if !files.contains(&entry.file) {
+                // Normalize path separators to forward slashes
+                let normalized_path = normalize_to_posix(&entry.file);
+                if !files.contains(&normalized_path) {
                     // Check if it's a text file before adding
-                    if is_text_file(working_log, &entry.file) {
-                        files.insert(entry.file.clone());
+                    if is_text_file(working_log, &normalized_path) {
+                        files.insert(normalized_path);
                     }
                 }
             }
@@ -392,11 +415,13 @@ fn get_all_tracked_files(
     // Ensure to always include all dirty files
     if let Some(ref dirty_files) = working_log.dirty_files {
         for file_path in dirty_files.keys() {
+            // Normalize path separators to forward slashes
+            let normalized_path = normalize_to_posix(file_path);
             // Only add if not already in the files list
-            if !results_for_tracked_files.contains(&file_path) {
+            if !results_for_tracked_files.contains(&normalized_path) {
                 // Check if it's a text file before adding
-                if is_text_file(working_log, &file_path) {
-                    results_for_tracked_files.push(file_path.clone());
+                if is_text_file(working_log, &normalized_path) {
+                    results_for_tracked_files.push(normalized_path);
                 }
             }
         }
@@ -1222,14 +1247,16 @@ mod tests {
 }
 
 fn is_text_file(working_log: &PersistedWorkingLog, path: &str) -> bool {
+    // Normalize path for dirty_files lookup
+    let normalized_path = normalize_to_posix(path);
     let skip_metadata_check = working_log
         .dirty_files
         .as_ref()
-        .map(|m| m.contains_key(path))
+        .map(|m| m.contains_key(&normalized_path))
         .unwrap_or(false);
 
     if !skip_metadata_check {
-        if let Ok(metadata) = std::fs::metadata(working_log.to_repo_absolute_path(path)) {
+        if let Ok(metadata) = std::fs::metadata(working_log.to_repo_absolute_path(&normalized_path)) {
             if !metadata.is_file() {
                 return false;
             }
@@ -1239,7 +1266,7 @@ fn is_text_file(working_log: &PersistedWorkingLog, path: &str) -> bool {
     }
 
     working_log
-        .read_current_file_content(path)
+        .read_current_file_content(&normalized_path)
         .map(|content| !content.chars().any(|c| c == '\0'))
         .unwrap_or(false)
 }
diff --git a/src/git/repository.rs b/src/git/repository.rs
index 7fcfe38e..5693905e 100644
--- a/src/git/repository.rs
+++ b/src/git/repository.rs
@@ -905,6 +905,12 @@ impl Repository {
         Ok(self.workdir.clone())
     }
 
+    /// Get the canonical (absolute, resolved) path of the working directory
+    /// On Windows, this uses the \\?\ UNC prefix format for reliable path comparisons
+    pub fn canonical_workdir(&self) -> &Path {
+        &self.canonical_workdir
+    }
+
     /// Check if a path is within the repository's working directory
     /// Uses canonical path comparison for reliability on Windows
     pub fn path_is_in_workdir(&self, path: &Path) -> bool {
diff --git a/src/utils.rs b/src/utils.rs
index 9bdb370c..06639e25 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -74,3 +74,28 @@ pub fn _print_diff(diff: &Diff, old_label: &str, new_label: &str) {
         println!("  No changes between {} and {}", old_label, new_label);
     }
 }
+
+/// Normalize a path to use POSIX-style forward slashes
+///
+/// Git expects paths with forward slashes, even on Windows. This function
+/// converts any backslashes to forward slashes for cross-platform compatibility.
+///
+/// # Arguments
+///
+/// * `path` - The path string to normalize (e.g., from `Path::to_string_lossy()`)
+///
+/// # Returns
+///
+/// A string with all backslashes replaced by forward slashes
+///
+/// # Example
+///
+/// ```
+/// let path = std::path::Path::new("src\\commands\\checkpoint.rs");
+/// let normalized = normalize_to_posix(&path.to_string_lossy());
+/// assert_eq!(normalized, "src/commands/checkpoint.rs");
+/// ```
+#[inline]
+pub fn normalize_to_posix(path: &str) -> String {
+    path.replace('\\', "/")
+}
\ No newline at end of file
diff --git a/tests/ai_tab.rs b/tests/ai_tab.rs
index 5711c1a1..cd11f3be 100644
--- a/tests/ai_tab.rs
+++ b/tests/ai_tab.rs
@@ -16,8 +16,13 @@ use git_ai::{
 fn run_ai_tab_checkpoint(repo: &TestRepo, hook_payload: serde_json::Value) {
     let hook_input = hook_payload.to_string();
     let args: Vec<&str> = vec!["checkpoint", "ai_tab", "--hook-input", hook_input.as_str()];
-    if let Err(err) = repo.git_ai(&args) {
-        panic!("ai_tab checkpoint failed: {}", err);
+    match repo.git_ai(&args) {
+        Ok(output) => {
+            println!("git_ai checkpoint output: {}", output);
+        }
+        Err(err) => {
+            panic!("ai_tab checkpoint failed: {}", err);
+        }
     }
 }
 
@@ -223,7 +228,7 @@ fn test_ai_tab_requires_non_empty_tool_and_model() {
 fn test_ai_tab_e2e_marks_ai_lines() {
     let repo = TestRepo::new();
     let relative_path = "notes_test.ts";
-    let file_path = repo.path().join(relative_path);
+    let file_path = repo.canonical_path().join(relative_path);
 
     let base_content = "console.log(\"hello world\");\n".to_string();
     fs::write(&file_path, &base_content).unwrap();
@@ -238,7 +243,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
             "hook_event_name": "before_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "will_edit_filepaths": [file_path_str.clone()],
             "dirty_files": {
                 file_path_str.clone(): base_content.clone()
@@ -256,7 +261,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
             "hook_event_name": "after_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "edited_filepaths": [file_path_str.clone()],
             "dirty_files": {
                 file_path_str.clone(): ai_content.clone()
@@ -278,13 +283,13 @@ fn test_ai_tab_e2e_marks_ai_lines() {
 fn test_ai_tab_e2e_handles_dirty_files_map() {
     let repo = TestRepo::new();
     let lib_relative_path = std::path::Path::new("src").join("lib.rs");
-    let lib_file_path = repo.path().join(lib_relative_path);
+    let lib_file_path = repo.canonical_path().join(lib_relative_path);
     // Create parent directory - handle Windows paths safely
     if let Some(parent) = lib_file_path.parent() {
         fs::create_dir_all(parent).unwrap();
     }
     let readme_relative_path = "README.md";
-    let readme_file_path = repo.path().join(readme_relative_path);
+    let readme_file_path = repo.canonical_path().join(readme_relative_path);
 
     let base_lib_content = "fn greet() {\n    println!(\"hello\");\n}\n".to_string();
     fs::write(&lib_file_path, &base_lib_content).unwrap();
@@ -299,6 +304,9 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
     let lib_file_path_str = lib_file_path.to_string_lossy().to_string();
     let readme_file_path_str = readme_file_path.to_string_lossy().to_string();
 
+    println!("lib_file_path_str: {}", lib_file_path_str);
+    println!("readme_file_path_str: {}", readme_file_path_str);
+
     // Before edit snapshot includes all dirty files (AI target plus unrelated human edits)
     run_ai_tab_checkpoint(
         &repo,
@@ -306,7 +314,7 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
             "hook_event_name": "before_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "will_edit_filepaths": [lib_file_path_str.clone()],
             "dirty_files": {
                 lib_file_path_str.clone(): base_lib_content.clone(),
@@ -327,7 +335,7 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
             "hook_event_name": "after_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "edited_filepaths": [lib_file_path_str.clone()],
             "dirty_files": {
                 lib_file_path_str.clone(): ai_content.clone(),
@@ -336,6 +344,18 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         }),
     );
 
+    // Debug: Check working logs before commit
+    let working_logs = repo.current_working_logs();
+    if let Ok(checkpoints) = working_logs.read_all_checkpoints() {
+        println!("Checkpoints before commit: {}", checkpoints.len());
+        for (i, cp) in checkpoints.iter().enumerate() {
+            println!("Checkpoint {}: kind={:?}, entries={}", i, cp.kind, cp.entries.len());
+            for entry in &cp.entries {
+                println!("  File: {}, attributions={}", entry.file, entry.attributions.len());
+            }
+        }
+    }
+
     repo.stage_all_and_commit("Record AI tab completion while other files dirty").unwrap();
 
     let mut file = repo.filename(&std::path::Path::new("src").join("lib.rs").to_string_lossy());
diff --git a/tests/repos/test_repo.rs b/tests/repos/test_repo.rs
index e0cc0560..da6798de 100644
--- a/tests/repos/test_repo.rs
+++ b/tests/repos/test_repo.rs
@@ -39,6 +39,10 @@ impl TestRepo {
         &self.path
     }
 
+    pub fn canonical_path(&self) -> PathBuf {
+        self.path.canonicalize().expect("failed to canonicalize test repo path")
+    }
+
     pub fn stats(&self) -> Result<CommitStats, String> {
         let mut stats = self.git_ai(&["stats", "--json"]).unwrap();
         stats = stats.split("}}}").next().unwrap().to_string() + "}}}";

From 2eda272b4b43d06343c92177356f8dea64d6f021 Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Sat, 8 Nov 2025 10:39:52 -0500
Subject: [PATCH 04/19] fix doc error

---
 src/utils.rs | 21 +--------------------
 1 file changed, 1 insertion(+), 20 deletions(-)

diff --git a/src/utils.rs b/src/utils.rs
index 06639e25..ab8cd594 100644
--- a/src/utils.rs
+++ b/src/utils.rs
@@ -75,26 +75,7 @@ pub fn _print_diff(diff: &Diff, old_label: &str, new_label: &str) {
     }
 }
 
-/// Normalize a path to use POSIX-style forward slashes
-///
-/// Git expects paths with forward slashes, even on Windows. This function
-/// converts any backslashes to forward slashes for cross-platform compatibility.
-///
-/// # Arguments
-///
-/// * `path` - The path string to normalize (e.g., from `Path::to_string_lossy()`)
-///
-/// # Returns
-///
-/// A string with all backslashes replaced by forward slashes
-///
-/// # Example
-///
-/// ```
-/// let path = std::path::Path::new("src\\commands\\checkpoint.rs");
-/// let normalized = normalize_to_posix(&path.to_string_lossy());
-/// assert_eq!(normalized, "src/commands/checkpoint.rs");
-/// ```
+
 #[inline]
 pub fn normalize_to_posix(path: &str) -> String {
     path.replace('\\', "/")

From 7d2586067b9a28b017a77218ba5ee604c6796fb5 Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Sat, 8 Nov 2025 11:03:32 -0500
Subject: [PATCH 05/19] fix. use canocical repo root

---
 src/git/repo_storage.rs | 80 +++++++++++++++++++++++++++--------------
 1 file changed, 54 insertions(+), 26 deletions(-)

diff --git a/src/git/repo_storage.rs b/src/git/repo_storage.rs
index ce586b4d..a940875f 100644
--- a/src/git/repo_storage.rs
+++ b/src/git/repo_storage.rs
@@ -73,7 +73,17 @@ impl RepoStorage {
     pub fn working_log_for_base_commit(&self, sha: &str) -> PersistedWorkingLog {
         let working_log_dir = self.working_logs.join(sha);
         fs::create_dir_all(&working_log_dir).unwrap();
-        PersistedWorkingLog::new(working_log_dir, sha, self.repo_workdir.clone(), None)
+        let canonical_workdir = self
+            .repo_workdir
+            .canonicalize()
+            .unwrap_or_else(|_| self.repo_workdir.clone());
+        PersistedWorkingLog::new(
+            working_log_dir,
+            sha,
+            self.repo_workdir.clone(),
+            canonical_workdir,
+            None,
+        )
     }
 
     #[allow(dead_code)]
@@ -123,6 +133,9 @@ pub struct PersistedWorkingLog {
     #[allow(dead_code)]
     pub base_commit: String,
     pub repo_workdir: PathBuf,
+    /// Canonical (absolute, resolved) version of workdir for reliable path comparisons
+    /// On Windows, this uses the \\?\ UNC prefix format
+    pub canonical_workdir: PathBuf,
     pub dirty_files: Option<HashMap<String, String>>,
 }
 
@@ -131,12 +144,14 @@ impl PersistedWorkingLog {
         dir: PathBuf,
         base_commit: &str,
         repo_root: PathBuf,
+        canonical_workdir: PathBuf,
         dirty_files: Option<HashMap<String, String>>,
     ) -> Self {
         Self {
             dir,
             base_commit: base_commit.to_string(),
             repo_workdir: repo_root,
+            canonical_workdir,
             dirty_files,
         }
     }
@@ -144,9 +159,7 @@ impl PersistedWorkingLog {
     pub fn set_dirty_files(&mut self, dirty_files: Option<HashMap<String, String>>) {
         self.dirty_files = dirty_files.map(|map| {
             map.into_iter()
-                .map(|(file_path, content)| {
-                    (self.to_repo_relative_path(&file_path), content)
-                })
+                .map(|(file_path, content)| (self.to_repo_relative_path(&file_path), content))
                 .collect()
         });
     }
@@ -192,7 +205,10 @@ impl PersistedWorkingLog {
         if Path::new(file_path).is_absolute() {
             return file_path.to_string();
         }
-        self.repo_workdir.join(file_path).to_string_lossy().to_string()
+        self.repo_workdir
+            .join(file_path)
+            .to_string_lossy()
+            .to_string()
     }
 
     pub fn to_repo_relative_path(&self, file_path: &str) -> String {
@@ -201,23 +217,26 @@ impl PersistedWorkingLog {
         }
         let path = Path::new(file_path);
 
-        // Try without canonicalizing first
-        if path.starts_with(&self.repo_workdir) {
-            return path.strip_prefix(&self.repo_workdir).unwrap().to_string_lossy().to_string();
+        // Try canonical comparison first (most reliable, especially on Windows)
+        if let Ok(canonical_path) = path.canonicalize() {
+            if canonical_path.starts_with(&self.canonical_workdir) {
+                return canonical_path
+                    .strip_prefix(&self.canonical_workdir)
+                    .unwrap()
+                    .to_string_lossy()
+                    .to_string();
+            }
         }
 
-        // If we couldn't match yet, try canonicalizing both repo_workdir and the input path
-        let canonical_workdir = match self.repo_workdir.canonicalize() {
-            Ok(p) => p,
-            Err(_) => self.repo_workdir.clone(),
-        };
-        let canonical_path = match path.canonicalize() {
-            Ok(p) => p,
-            Err(_) => path.to_path_buf(),
-        };
-        if canonical_path.starts_with(&canonical_workdir) {
-            return canonical_path.strip_prefix(&canonical_workdir).unwrap().to_string_lossy().to_string();
+        // Fallback: try with non-canonical paths
+        if path.starts_with(&self.repo_workdir) {
+            return path
+                .strip_prefix(&self.repo_workdir)
+                .unwrap()
+                .to_string_lossy()
+                .to_string();
         }
+
         return file_path.to_string();
     }
 
@@ -400,7 +419,8 @@ mod tests {
         let tmp_repo = TmpRepo::new().expect("Failed to create tmp repo");
 
         // Create RepoStorage
-        let _repo_storage = RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
+        let _repo_storage =
+            RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
 
         // Verify .git/ai directory exists
         let ai_dir = tmp_repo.repo().path().join("ai");
@@ -433,7 +453,10 @@ mod tests {
         let tmp_repo = TmpRepo::new().expect("Failed to create tmp repo");
 
         // Create RepoStorage
-        let repo_storage = RepoStorage::for_repo_path(&tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
+        let repo_storage = RepoStorage::for_repo_path(
+            &tmp_repo.repo().path(),
+            &tmp_repo.repo().workdir().unwrap(),
+        );
 
         // Add some content to rewrite_log
         let rewrite_log_file = tmp_repo.repo().path().join("ai").join("rewrite_log");
@@ -467,7 +490,8 @@ mod tests {
         let tmp_repo = TmpRepo::new().expect("Failed to create tmp repo");
 
         // Create RepoStorage and PersistedWorkingLog
-        let repo_storage = RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
+        let repo_storage =
+            RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
         let working_log = repo_storage.working_log_for_base_commit("test-commit-sha");
 
         // Test persisting a file version
@@ -510,7 +534,8 @@ mod tests {
         let tmp_repo = TmpRepo::new().expect("Failed to create tmp repo");
 
         // Create RepoStorage and PersistedWorkingLog
-        let repo_storage = RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
+        let repo_storage =
+            RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
         let working_log = repo_storage.working_log_for_base_commit("test-commit-sha");
 
         // Create a test checkpoint
@@ -566,7 +591,8 @@ mod tests {
         let tmp_repo = TmpRepo::new().expect("Failed to create tmp repo");
 
         // Create RepoStorage and PersistedWorkingLog
-        let repo_storage = RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
+        let repo_storage =
+            RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
         let working_log = repo_storage.working_log_for_base_commit("test-commit-sha");
 
         // Build three checkpoints: missing version, wrong version, and correct version
@@ -618,7 +644,8 @@ mod tests {
         let tmp_repo = TmpRepo::new().expect("Failed to create tmp repo");
 
         // Create RepoStorage and PersistedWorkingLog
-        let repo_storage = RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
+        let repo_storage =
+            RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
         let working_log = repo_storage.working_log_for_base_commit("test-commit-sha");
 
         // Add some blobs
@@ -686,7 +713,8 @@ mod tests {
         let tmp_repo = TmpRepo::new().expect("Failed to create tmp repo");
 
         // Create RepoStorage
-        let repo_storage = RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
+        let repo_storage =
+            RepoStorage::for_repo_path(tmp_repo.repo().path(), &tmp_repo.repo().workdir().unwrap());
 
         // Create working log for a specific commit
         let commit_sha = "abc123def456";

From 337074d7201019a3ade1dd25ab10c75dac044442 Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Sat, 8 Nov 2025 11:10:49 -0500
Subject: [PATCH 06/19] fix ests

---
 tests/ai_tab.rs | 60 ++++++++++++++++++-------------------------------
 1 file changed, 22 insertions(+), 38 deletions(-)

diff --git a/tests/ai_tab.rs b/tests/ai_tab.rs
index cd11f3be..8db65e93 100644
--- a/tests/ai_tab.rs
+++ b/tests/ai_tab.rs
@@ -16,13 +16,8 @@ use git_ai::{
 fn run_ai_tab_checkpoint(repo: &TestRepo, hook_payload: serde_json::Value) {
     let hook_input = hook_payload.to_string();
     let args: Vec<&str> = vec!["checkpoint", "ai_tab", "--hook-input", hook_input.as_str()];
-    match repo.git_ai(&args) {
-        Ok(output) => {
-            println!("git_ai checkpoint output: {}", output);
-        }
-        Err(err) => {
-            panic!("ai_tab checkpoint failed: {}", err);
-        }
+    if let Err(err) = repo.git_ai(&args) {
+        panic!("ai_tab checkpoint failed: {}", err);
     }
 }
 
@@ -135,10 +130,7 @@ fn test_ai_tab_after_edit_checkpoint_includes_dirty_files_and_paths() {
     let edited = result
         .edited_filepaths
         .expect("after_edit should include edited filepaths");
-    assert_eq!(
-        edited,
-        vec!["/Users/test/project/src/main.rs".to_string()]
-    );
+    assert_eq!(edited, vec!["/Users/test/project/src/main.rs".to_string()]);
 
     let dirty_files = result
         .dirty_files
@@ -173,7 +165,10 @@ fn test_ai_tab_rejects_invalid_hook_event() {
                 message
             );
         }
-        other => panic!("expected PresetError for invalid hook_event_name, got {:?}", other),
+        other => panic!(
+            "expected PresetError for invalid hook_event_name, got {:?}",
+            other
+        ),
     }
 }
 
@@ -228,7 +223,7 @@ fn test_ai_tab_requires_non_empty_tool_and_model() {
 fn test_ai_tab_e2e_marks_ai_lines() {
     let repo = TestRepo::new();
     let relative_path = "notes_test.ts";
-    let file_path = repo.canonical_path().join(relative_path);
+    let file_path = repo.path().join(relative_path);
 
     let base_content = "console.log(\"hello world\");\n".to_string();
     fs::write(&file_path, &base_content).unwrap();
@@ -243,7 +238,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
             "hook_event_name": "before_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.canonical_path().to_string_lossy(),
+            "repo_working_dir": repo.path().to_string_lossy(),
             "will_edit_filepaths": [file_path_str.clone()],
             "dirty_files": {
                 file_path_str.clone(): base_content.clone()
@@ -252,7 +247,9 @@ fn test_ai_tab_e2e_marks_ai_lines() {
     );
 
     // AI tab inserts new lines alongside the existing content
-    let ai_content = "console.log(\"hello world\");\n// Log hello world\nconsole.log(\"hello from ai\");\n".to_string();
+    let ai_content =
+        "console.log(\"hello world\");\n// Log hello world\nconsole.log(\"hello from ai\");\n"
+            .to_string();
     fs::write(&file_path, &ai_content).unwrap();
 
     run_ai_tab_checkpoint(
@@ -261,7 +258,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
             "hook_event_name": "after_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.canonical_path().to_string_lossy(),
+            "repo_working_dir": repo.path().to_string_lossy(),
             "edited_filepaths": [file_path_str.clone()],
             "dirty_files": {
                 file_path_str.clone(): ai_content.clone()
@@ -269,7 +266,8 @@ fn test_ai_tab_e2e_marks_ai_lines() {
         }),
     );
 
-    repo.stage_all_and_commit("Accept AI tab completion").unwrap();
+    repo.stage_all_and_commit("Accept AI tab completion")
+        .unwrap();
 
     let mut file = repo.filename(relative_path);
     file.assert_lines_and_blame(lines![
@@ -283,13 +281,13 @@ fn test_ai_tab_e2e_marks_ai_lines() {
 fn test_ai_tab_e2e_handles_dirty_files_map() {
     let repo = TestRepo::new();
     let lib_relative_path = std::path::Path::new("src").join("lib.rs");
-    let lib_file_path = repo.canonical_path().join(lib_relative_path);
+    let lib_file_path = repo.path().join(lib_relative_path);
     // Create parent directory - handle Windows paths safely
     if let Some(parent) = lib_file_path.parent() {
         fs::create_dir_all(parent).unwrap();
     }
     let readme_relative_path = "README.md";
-    let readme_file_path = repo.canonical_path().join(readme_relative_path);
+    let readme_file_path = repo.path().join(readme_relative_path);
 
     let base_lib_content = "fn greet() {\n    println!(\"hello\");\n}\n".to_string();
     fs::write(&lib_file_path, &base_lib_content).unwrap();
@@ -304,9 +302,6 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
     let lib_file_path_str = lib_file_path.to_string_lossy().to_string();
     let readme_file_path_str = readme_file_path.to_string_lossy().to_string();
 
-    println!("lib_file_path_str: {}", lib_file_path_str);
-    println!("readme_file_path_str: {}", readme_file_path_str);
-
     // Before edit snapshot includes all dirty files (AI target plus unrelated human edits)
     run_ai_tab_checkpoint(
         &repo,
@@ -314,7 +309,7 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
             "hook_event_name": "before_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.canonical_path().to_string_lossy(),
+            "repo_working_dir": repo.path().to_string_lossy(),
             "will_edit_filepaths": [lib_file_path_str.clone()],
             "dirty_files": {
                 lib_file_path_str.clone(): base_lib_content.clone(),
@@ -335,7 +330,7 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
             "hook_event_name": "after_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.canonical_path().to_string_lossy(),
+            "repo_working_dir": repo.path().to_string_lossy(),
             "edited_filepaths": [lib_file_path_str.clone()],
             "dirty_files": {
                 lib_file_path_str.clone(): ai_content.clone(),
@@ -344,19 +339,8 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         }),
     );
 
-    // Debug: Check working logs before commit
-    let working_logs = repo.current_working_logs();
-    if let Ok(checkpoints) = working_logs.read_all_checkpoints() {
-        println!("Checkpoints before commit: {}", checkpoints.len());
-        for (i, cp) in checkpoints.iter().enumerate() {
-            println!("Checkpoint {}: kind={:?}, entries={}", i, cp.kind, cp.entries.len());
-            for entry in &cp.entries {
-                println!("  File: {}, attributions={}", entry.file, entry.attributions.len());
-            }
-        }
-    }
-
-    repo.stage_all_and_commit("Record AI tab completion while other files dirty").unwrap();
+    repo.stage_all_and_commit("Record AI tab completion while other files dirty")
+        .unwrap();
 
     let mut file = repo.filename(&std::path::Path::new("src").join("lib.rs").to_string_lossy());
     file.assert_lines_and_blame(lines![
@@ -367,4 +351,4 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         "    println!(\"from ai\");".ai(),
         "}".ai(),
     ]);
-}
\ No newline at end of file
+}

From a5bd40ca93a6106c2ed53dabefa4f70b48d106f4 Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Sat, 8 Nov 2025 12:37:11 -0500
Subject: [PATCH 07/19] more debugging

---
 tests/ai_tab.rs | 56 +++++++++++++++++++++++++++++++------------------
 1 file changed, 36 insertions(+), 20 deletions(-)

diff --git a/tests/ai_tab.rs b/tests/ai_tab.rs
index 8db65e93..91d07f41 100644
--- a/tests/ai_tab.rs
+++ b/tests/ai_tab.rs
@@ -16,8 +16,13 @@ use git_ai::{
 fn run_ai_tab_checkpoint(repo: &TestRepo, hook_payload: serde_json::Value) {
     let hook_input = hook_payload.to_string();
     let args: Vec<&str> = vec!["checkpoint", "ai_tab", "--hook-input", hook_input.as_str()];
-    if let Err(err) = repo.git_ai(&args) {
-        panic!("ai_tab checkpoint failed: {}", err);
+    match repo.git_ai(&args) {
+        Ok(output) => {
+            println!("git_ai checkpoint output: {}", output);
+        }
+        Err(err) => {
+            panic!("ai_tab checkpoint failed: {}", err);
+        }
     }
 }
 
@@ -130,7 +135,10 @@ fn test_ai_tab_after_edit_checkpoint_includes_dirty_files_and_paths() {
     let edited = result
         .edited_filepaths
         .expect("after_edit should include edited filepaths");
-    assert_eq!(edited, vec!["/Users/test/project/src/main.rs".to_string()]);
+    assert_eq!(
+        edited,
+        vec!["/Users/test/project/src/main.rs".to_string()]
+    );
 
     let dirty_files = result
         .dirty_files
@@ -165,10 +173,7 @@ fn test_ai_tab_rejects_invalid_hook_event() {
                 message
             );
         }
-        other => panic!(
-            "expected PresetError for invalid hook_event_name, got {:?}",
-            other
-        ),
+        other => panic!("expected PresetError for invalid hook_event_name, got {:?}", other),
     }
 }
 
@@ -223,7 +228,7 @@ fn test_ai_tab_requires_non_empty_tool_and_model() {
 fn test_ai_tab_e2e_marks_ai_lines() {
     let repo = TestRepo::new();
     let relative_path = "notes_test.ts";
-    let file_path = repo.path().join(relative_path);
+    let file_path = repo.canonical_path().join(relative_path);
 
     let base_content = "console.log(\"hello world\");\n".to_string();
     fs::write(&file_path, &base_content).unwrap();
@@ -238,7 +243,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
             "hook_event_name": "before_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "will_edit_filepaths": [file_path_str.clone()],
             "dirty_files": {
                 file_path_str.clone(): base_content.clone()
@@ -247,9 +252,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
     );
 
     // AI tab inserts new lines alongside the existing content
-    let ai_content =
-        "console.log(\"hello world\");\n// Log hello world\nconsole.log(\"hello from ai\");\n"
-            .to_string();
+    let ai_content = "console.log(\"hello world\");\n// Log hello world\nconsole.log(\"hello from ai\");\n".to_string();
     fs::write(&file_path, &ai_content).unwrap();
 
     run_ai_tab_checkpoint(
@@ -258,7 +261,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
             "hook_event_name": "after_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "edited_filepaths": [file_path_str.clone()],
             "dirty_files": {
                 file_path_str.clone(): ai_content.clone()
@@ -266,8 +269,7 @@ fn test_ai_tab_e2e_marks_ai_lines() {
         }),
     );
 
-    repo.stage_all_and_commit("Accept AI tab completion")
-        .unwrap();
+    repo.stage_all_and_commit("Accept AI tab completion").unwrap();
 
     let mut file = repo.filename(relative_path);
     file.assert_lines_and_blame(lines![
@@ -302,6 +304,9 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
     let lib_file_path_str = lib_file_path.to_string_lossy().to_string();
     let readme_file_path_str = readme_file_path.to_string_lossy().to_string();
 
+    println!("lib_file_path_str: {}", lib_file_path_str);
+    println!("readme_file_path_str: {}", readme_file_path_str);
+
     // Before edit snapshot includes all dirty files (AI target plus unrelated human edits)
     run_ai_tab_checkpoint(
         &repo,
@@ -309,7 +314,7 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
             "hook_event_name": "before_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "will_edit_filepaths": [lib_file_path_str.clone()],
             "dirty_files": {
                 lib_file_path_str.clone(): base_lib_content.clone(),
@@ -330,7 +335,7 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
             "hook_event_name": "after_edit",
             "tool": "github-copilot-tab",
             "model": "default",
-            "repo_working_dir": repo.path().to_string_lossy(),
+            "repo_working_dir": repo.canonical_path().to_string_lossy(),
             "edited_filepaths": [lib_file_path_str.clone()],
             "dirty_files": {
                 lib_file_path_str.clone(): ai_content.clone(),
@@ -339,8 +344,19 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         }),
     );
 
-    repo.stage_all_and_commit("Record AI tab completion while other files dirty")
-        .unwrap();
+    // Debug: Check working logs before commit
+    let working_logs = repo.current_working_logs();
+    if let Ok(checkpoints) = working_logs.read_all_checkpoints() {
+        println!("Checkpoints before commit: {}", checkpoints.len());
+        for (i, cp) in checkpoints.iter().enumerate() {
+            println!("Checkpoint {}: kind={:?}, entries={}", i, cp.kind, cp.entries.len());
+            for entry in &cp.entries {
+                println!("  File: {}, attributions={}", entry.file, entry.attributions.len());
+            }
+        }
+    }
+
+    repo.stage_all_and_commit("Record AI tab completion while other files dirty").unwrap();
 
     let mut file = repo.filename(&std::path::Path::new("src").join("lib.rs").to_string_lossy());
     file.assert_lines_and_blame(lines![
@@ -351,4 +367,4 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         "    println!(\"from ai\");".ai(),
         "}".ai(),
     ]);
-}
+}
\ No newline at end of file

From 08902c88904107151f7fb39567185ac5ae12249d Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 17:10:15 -0500
Subject: [PATCH 08/19] close

---
 src/git/repo_storage.rs | 18 ++++++++++++++----
 tests/ai_tab.rs         | 29 +++++++++++++++++++----------
 2 files changed, 33 insertions(+), 14 deletions(-)

diff --git a/src/git/repo_storage.rs b/src/git/repo_storage.rs
index a940875f..921af746 100644
--- a/src/git/repo_storage.rs
+++ b/src/git/repo_storage.rs
@@ -3,7 +3,7 @@ use crate::authorship::authorship_log::PromptRecord;
 use crate::authorship::working_log::{CHECKPOINT_API_VERSION, Checkpoint, CheckpointKind};
 use crate::error::GitAiError;
 use crate::git::rewrite_log::{RewriteLogEvent, append_event_to_file};
-use crate::utils::debug_log;
+use crate::utils::{debug_log, normalize_to_posix};
 use serde::{Deserialize, Serialize};
 use sha2::{Digest, Sha256};
 use std::collections::{HashMap, HashSet};
@@ -157,11 +157,21 @@ impl PersistedWorkingLog {
     }
 
     pub fn set_dirty_files(&mut self, dirty_files: Option<HashMap<String, String>>) {
-        self.dirty_files = dirty_files.map(|map| {
+        println!("pre_transform dirty_files: {:?}", dirty_files);
+
+        let normalized_dirty_files = dirty_files.map(|map| {
             map.into_iter()
-                .map(|(file_path, content)| (self.to_repo_relative_path(&file_path), content))
-                .collect()
+                .map(|(file_path, content)| {
+                    let relative_path = self.to_repo_relative_path(&file_path);
+                    let normalized_path = normalize_to_posix(&relative_path);
+                    (normalized_path, content)
+                })
+                .collect::<HashMap<_, _>>()
         });
+
+        self.dirty_files = normalized_dirty_files;
+
+        println!("setdirty_files: {:?}", self.dirty_files);
     }
 
     pub fn reset_working_log(&self) -> Result<(), GitAiError> {
diff --git a/tests/ai_tab.rs b/tests/ai_tab.rs
index 91d07f41..4091a874 100644
--- a/tests/ai_tab.rs
+++ b/tests/ai_tab.rs
@@ -307,6 +307,9 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
     println!("lib_file_path_str: {}", lib_file_path_str);
     println!("readme_file_path_str: {}", readme_file_path_str);
 
+    let working_logs = repo.current_working_logs();
+    println!("dirty_files: {:?}", working_logs.dirty_files);
+
     // Before edit snapshot includes all dirty files (AI target plus unrelated human edits)
     run_ai_tab_checkpoint(
         &repo,
@@ -329,6 +332,9 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
             .to_string();
     fs::write(&lib_file_path, &ai_content).unwrap();
 
+    let working_logs = repo.current_working_logs();
+    println!("dirty_files: {:?}", working_logs.dirty_files);
+
     run_ai_tab_checkpoint(
         &repo,
         json!({
@@ -344,17 +350,20 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         }),
     );
 
-    // Debug: Check working logs before commit
+    // // Debug: Check working logs before commit
+    // let working_logs = repo.current_working_logs();
+    // if let Ok(checkpoints) = working_logs.read_all_checkpoints() {
+    //     println!("Checkpoints before commit: {}", checkpoints.len());
+    //     for (i, cp) in checkpoints.iter().enumerate() {
+    //         println!("Checkpoint {}: kind={:?}, entries={}", i, cp.kind, cp.entries.len());
+    //         for entry in &cp.entries {
+    //             println!("  File: {}, attributions={}", entry.file, entry.attributions.len());
+    //         }
+    //     }
+    // }
+
     let working_logs = repo.current_working_logs();
-    if let Ok(checkpoints) = working_logs.read_all_checkpoints() {
-        println!("Checkpoints before commit: {}", checkpoints.len());
-        for (i, cp) in checkpoints.iter().enumerate() {
-            println!("Checkpoint {}: kind={:?}, entries={}", i, cp.kind, cp.entries.len());
-            for entry in &cp.entries {
-                println!("  File: {}, attributions={}", entry.file, entry.attributions.len());
-            }
-        }
-    }
+    println!("dirty_files: {:?}", working_logs.dirty_files);
 
     repo.stage_all_and_commit("Record AI tab completion while other files dirty").unwrap();
 

From a0a9804bdc64615ccf1ee4f69b0f38eb56e05860 Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 18:27:33 -0500
Subject: [PATCH 09/19] windows working. fix test helper

---
 tests/ai_tab.rs          | 19 ++++++-------------
 tests/repos/test_file.rs | 38 +++++++++++++++++++++++++++++---------
 tests/repos/test_repo.rs |  4 ++--
 3 files changed, 37 insertions(+), 24 deletions(-)

diff --git a/tests/ai_tab.rs b/tests/ai_tab.rs
index 4091a874..9aae3987 100644
--- a/tests/ai_tab.rs
+++ b/tests/ai_tab.rs
@@ -350,24 +350,17 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         }),
     );
 
-    // // Debug: Check working logs before commit
-    // let working_logs = repo.current_working_logs();
-    // if let Ok(checkpoints) = working_logs.read_all_checkpoints() {
-    //     println!("Checkpoints before commit: {}", checkpoints.len());
-    //     for (i, cp) in checkpoints.iter().enumerate() {
-    //         println!("Checkpoint {}: kind={:?}, entries={}", i, cp.kind, cp.entries.len());
-    //         for entry in &cp.entries {
-    //             println!("  File: {}, attributions={}", entry.file, entry.attributions.len());
-    //         }
-    //     }
-    // }
 
     let working_logs = repo.current_working_logs();
     println!("dirty_files: {:?}", working_logs.dirty_files);
 
-    repo.stage_all_and_commit("Record AI tab completion while other files dirty").unwrap();
+    let commit_result = repo.stage_all_and_commit("Record AI tab completion while other files dirty").unwrap();
+    println!("COMMIT OUTPUT: {}", commit_result.stdout);
 
-    let mut file = repo.filename(&std::path::Path::new("src").join("lib.rs").to_string_lossy());
+
+    commit_result.print_authorship();
+
+    let mut file = repo.filename("src/lib.rs");
     file.assert_lines_and_blame(lines![
         "fn greet() {".human(),
         "    println!(\"hello\");".human(),
diff --git a/tests/repos/test_file.rs b/tests/repos/test_file.rs
index f0de88de..9a641bdd 100644
--- a/tests/repos/test_file.rs
+++ b/tests/repos/test_file.rs
@@ -120,8 +120,12 @@ impl<'a> TestFile<'a> {
             };
         }
 
-        // Run blame to get authorship
-        let filename = file_path.to_str().expect("valid path");
+        // Run blame to get authorship - use relative path from repo root
+        let filename = file_path
+            .strip_prefix(&repo.path)
+            .expect("file path should be within repo")
+            .to_str()
+            .expect("valid path");
         let blame_result = repo.git_ai(&["blame", filename]);
 
         let lines = if let Ok(blame_output) = blame_result {
@@ -213,7 +217,11 @@ impl<'a> TestFile<'a> {
     }
 
     pub fn assert_blame_snapshot(&self) {
-        let filename = self.file_path.to_str().expect("valid path");
+        let filename = self.file_path
+            .strip_prefix(&self.repo.path)
+            .expect("file path should be within repo")
+            .to_str()
+            .expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
@@ -226,8 +234,12 @@ impl<'a> TestFile<'a> {
     pub fn assert_lines_and_blame<T: Into<ExpectedLine>>(&mut self, lines: Vec<T>) {
         let expected_lines: Vec<ExpectedLine> = lines.into_iter().map(|l| l.into()).collect();
 
-        // Get blame output
-        let filename = self.file_path.to_str().expect("valid path");
+        // Get blame output - use relative path from repo root
+        let filename = self.file_path
+            .strip_prefix(&self.repo.path)
+            .expect("file path should be within repo")
+            .to_str()
+            .expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
@@ -300,8 +312,12 @@ impl<'a> TestFile<'a> {
     pub fn assert_committed_lines<T: Into<ExpectedLine>>(&mut self, lines: Vec<T>) {
         let expected_lines: Vec<ExpectedLine> = lines.into_iter().map(|l| l.into()).collect();
 
-        // Get blame output
-        let filename = self.file_path.to_str().expect("valid path");
+        // Get blame output - use relative path from repo root
+        let filename = self.file_path
+            .strip_prefix(&self.repo.path)
+            .expect("file path should be within repo")
+            .to_str()
+            .expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
@@ -430,8 +446,12 @@ impl<'a> TestFile<'a> {
 
     /// Assert that the file at the given path matches the expected contents and authorship
     pub fn assert_blame_contents_expected(&self) {
-        // Get blame output
-        let filename = self.file_path.to_str().expect("valid path");
+        // Get blame output - use relative path from repo root
+        let filename = self.file_path
+            .strip_prefix(&self.repo.path)
+            .expect("file path should be within repo")
+            .to_str()
+            .expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
diff --git a/tests/repos/test_repo.rs b/tests/repos/test_repo.rs
index da6798de..fc876767 100644
--- a/tests/repos/test_repo.rs
+++ b/tests/repos/test_repo.rs
@@ -14,7 +14,7 @@ use super::test_file::TestFile;
 
 #[derive(Clone, Debug)]
 pub struct TestRepo {
-    path: PathBuf,
+    pub path: PathBuf,
 }
 
 impl TestRepo {
@@ -216,7 +216,7 @@ impl TestRepo {
     }
 
     pub fn stage_all_and_commit(&self, message: &str) -> Result<NewCommit, String> {
-        self.git(&["add", "-A"]).expect("add --all should succeed");
+        println!("stage_all_and_commit: {:?}", self.git(&["add", "-A"]).expect("add --all should succeed"));
         self.commit(message)
     }
 

From f3cf9722dd6cb47d14da2ebb347cf148c9be5e9d Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 18:40:45 -0500
Subject: [PATCH 10/19] relitivize blame

---
 src/commands/blame.rs | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/commands/blame.rs b/src/commands/blame.rs
index bb31486c..c62df72b 100644
--- a/src/commands/blame.rs
+++ b/src/commands/blame.rs
@@ -5,6 +5,8 @@ use crate::error::GitAiError;
 use crate::git::refs::get_reference_as_authorship_log_v3;
 use crate::git::repository::Repository;
 use crate::git::repository::exec_git;
+#[cfg(windows)]
+use crate::utils::normalize_to_posix;
 use chrono::{DateTime, FixedOffset, TimeZone, Utc};
 use std::collections::HashMap;
 use std::fs;
@@ -194,6 +196,12 @@ impl Repository {
             file_path.to_string()
         };
 
+        #[cfg(windows)]
+        let relative_file_path = normalize_to_posix(&relative_file_path);
+
+        #[cfg(not(windows))]
+        let relative_file_path = relative_file_path;
+
         let abs_file_path = repo_root.join(&relative_file_path);
 
         // Validate that the file exists

From 85129e6584eba6ac55f5ae326fbb3664a1bc9d45 Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 18:56:56 -0500
Subject: [PATCH 11/19] fix

---
 src/commands/blame.rs | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/commands/blame.rs b/src/commands/blame.rs
index c62df72b..a6db9a60 100644
--- a/src/commands/blame.rs
+++ b/src/commands/blame.rs
@@ -196,13 +196,23 @@ impl Repository {
             file_path.to_string()
         };
 
+        // do this before normalizing the path
+        let abs_file_path = repo_root.join(&relative_file_path);
+
+
         #[cfg(windows)]
-        let relative_file_path = normalize_to_posix(&relative_file_path);
+        let relative_file_path = {
+            let normalized = normalize_to_posix(&relative_file_path);
+            // Strip leading ./ or .\ if present
+            normalized.strip_prefix("./").unwrap_or(&normalized).to_string()
+        };
 
         #[cfg(not(windows))]
-        let relative_file_path = relative_file_path;
+        let relative_file_path = {
+            // Also strip leading ./ on non-Windows for consistency
+            relative_file_path.strip_prefix("./").unwrap_or(&relative_file_path).to_string()
+        };
 
-        let abs_file_path = repo_root.join(&relative_file_path);
 
         // Validate that the file exists
         if !abs_file_path.exists() {

From 6cfa65dddac75df31ac744ae73246e2568d5fff9 Mon Sep 17 00:00:00 2001
From: "acunniffe@gmail.com" <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 18:58:37 -0500
Subject: [PATCH 12/19] fix

---
 tests/repos/test_file.rs | 38 +++++++++-----------------------------
 tests/repos/test_repo.rs |  4 ++--
 2 files changed, 11 insertions(+), 31 deletions(-)

diff --git a/tests/repos/test_file.rs b/tests/repos/test_file.rs
index 9a641bdd..f0de88de 100644
--- a/tests/repos/test_file.rs
+++ b/tests/repos/test_file.rs
@@ -120,12 +120,8 @@ impl<'a> TestFile<'a> {
             };
         }
 
-        // Run blame to get authorship - use relative path from repo root
-        let filename = file_path
-            .strip_prefix(&repo.path)
-            .expect("file path should be within repo")
-            .to_str()
-            .expect("valid path");
+        // Run blame to get authorship
+        let filename = file_path.to_str().expect("valid path");
         let blame_result = repo.git_ai(&["blame", filename]);
 
         let lines = if let Ok(blame_output) = blame_result {
@@ -217,11 +213,7 @@ impl<'a> TestFile<'a> {
     }
 
     pub fn assert_blame_snapshot(&self) {
-        let filename = self.file_path
-            .strip_prefix(&self.repo.path)
-            .expect("file path should be within repo")
-            .to_str()
-            .expect("valid path");
+        let filename = self.file_path.to_str().expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
@@ -234,12 +226,8 @@ impl<'a> TestFile<'a> {
     pub fn assert_lines_and_blame<T: Into<ExpectedLine>>(&mut self, lines: Vec<T>) {
         let expected_lines: Vec<ExpectedLine> = lines.into_iter().map(|l| l.into()).collect();
 
-        // Get blame output - use relative path from repo root
-        let filename = self.file_path
-            .strip_prefix(&self.repo.path)
-            .expect("file path should be within repo")
-            .to_str()
-            .expect("valid path");
+        // Get blame output
+        let filename = self.file_path.to_str().expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
@@ -312,12 +300,8 @@ impl<'a> TestFile<'a> {
     pub fn assert_committed_lines<T: Into<ExpectedLine>>(&mut self, lines: Vec<T>) {
         let expected_lines: Vec<ExpectedLine> = lines.into_iter().map(|l| l.into()).collect();
 
-        // Get blame output - use relative path from repo root
-        let filename = self.file_path
-            .strip_prefix(&self.repo.path)
-            .expect("file path should be within repo")
-            .to_str()
-            .expect("valid path");
+        // Get blame output
+        let filename = self.file_path.to_str().expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
@@ -446,12 +430,8 @@ impl<'a> TestFile<'a> {
 
     /// Assert that the file at the given path matches the expected contents and authorship
     pub fn assert_blame_contents_expected(&self) {
-        // Get blame output - use relative path from repo root
-        let filename = self.file_path
-            .strip_prefix(&self.repo.path)
-            .expect("file path should be within repo")
-            .to_str()
-            .expect("valid path");
+        // Get blame output
+        let filename = self.file_path.to_str().expect("valid path");
         let blame_output = self
             .repo
             .git_ai(&["blame", filename])
diff --git a/tests/repos/test_repo.rs b/tests/repos/test_repo.rs
index fc876767..da6798de 100644
--- a/tests/repos/test_repo.rs
+++ b/tests/repos/test_repo.rs
@@ -14,7 +14,7 @@ use super::test_file::TestFile;
 
 #[derive(Clone, Debug)]
 pub struct TestRepo {
-    pub path: PathBuf,
+    path: PathBuf,
 }
 
 impl TestRepo {
@@ -216,7 +216,7 @@ impl TestRepo {
     }
 
     pub fn stage_all_and_commit(&self, message: &str) -> Result<NewCommit, String> {
-        println!("stage_all_and_commit: {:?}", self.git(&["add", "-A"]).expect("add --all should succeed"));
+        self.git(&["add", "-A"]).expect("add --all should succeed");
         self.commit(message)
     }
 

From a6373790070fc586c1355c8d398b8b0a9dc589b2 Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 19:11:29 -0500
Subject: [PATCH 13/19] add to bare repo constructor

---
 ...__stats__tests__markdown_stats_display.snap.new |  6 ++++++
 src/commands/blame.rs                              | 10 ++++++++--
 src/git/repo_storage.rs                            |  8 ++++----
 src/git/repository.rs                              | 14 ++++++++------
 4 files changed, 26 insertions(+), 12 deletions(-)
 create mode 100644 src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new

diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new
new file mode 100644
index 00000000..91cc02aa
--- /dev/null
+++ b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new
@@ -0,0 +1,6 @@
+---
+source: src/authorship/stats.rs
+assertion_line: 768
+expression: mixed_output
+---
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █████████████░░░░░░░  63%\n🤝 mixed  ░░░░░░░░░░░░░██████████  50%\n🤖 ai     ░░░░░░░░░░░░░░██████  31%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 4.0 lines generated for every 1 accepted\n- 1200 minutes waiting for AI \n\n</details>"
diff --git a/src/commands/blame.rs b/src/commands/blame.rs
index 86d5b569..ce024af7 100644
--- a/src/commands/blame.rs
+++ b/src/commands/blame.rs
@@ -201,13 +201,19 @@ impl Repository {
         let relative_file_path = {
             let normalized = normalize_to_posix(&relative_file_path);
             // Strip leading ./ or .\ if present
-            normalized.strip_prefix("./").unwrap_or(&normalized).to_string()
+            normalized
+                .strip_prefix("./")
+                .unwrap_or(&normalized)
+                .to_string()
         };
 
         #[cfg(not(windows))]
         let relative_file_path = {
             // Also strip leading ./ on non-Windows for consistency
-            relative_file_path.strip_prefix("./").unwrap_or(&relative_file_path).to_string()
+            relative_file_path
+                .strip_prefix("./")
+                .unwrap_or(&relative_file_path)
+                .to_string()
         };
 
         // Read file content either from a specific commit or from working directory
diff --git a/src/git/repo_storage.rs b/src/git/repo_storage.rs
index 01521143..355ac7a4 100644
--- a/src/git/repo_storage.rs
+++ b/src/git/repo_storage.rs
@@ -240,18 +240,18 @@ impl PersistedWorkingLog {
         // On Windows, this uses the canonical_workdir that was pre-computed
         #[cfg(windows)]
         let canonical_workdir = &self.canonical_workdir;
-        
+
         #[cfg(not(windows))]
         let canonical_workdir = match self.repo_workdir.canonicalize() {
             Ok(p) => p,
             Err(_) => self.repo_workdir.clone(),
         };
-        
+
         let canonical_path = match path.canonicalize() {
             Ok(p) => p,
             Err(_) => path.to_path_buf(),
         };
-        
+
         #[cfg(windows)]
         if canonical_path.starts_with(canonical_workdir) {
             return canonical_path
@@ -260,7 +260,7 @@ impl PersistedWorkingLog {
                 .to_string_lossy()
                 .to_string();
         }
-        
+
         #[cfg(not(windows))]
         if canonical_path.starts_with(&canonical_workdir) {
             return canonical_path
diff --git a/src/git/repository.rs b/src/git/repository.rs
index 5ce76c90..30b1d8af 100644
--- a/src/git/repository.rs
+++ b/src/git/repository.rs
@@ -931,11 +931,11 @@ impl Repository {
         if let Ok(canonical_path) = path.canonicalize() {
             return canonical_path.starts_with(&self.canonical_workdir);
         }
-        
+
         // Fallback for paths that don't exist yet: normalize by resolving .. and .
-        let normalized = path.components().fold(
-            std::path::PathBuf::new(),
-            |mut acc, component| {
+        let normalized = path
+            .components()
+            .fold(std::path::PathBuf::new(), |mut acc, component| {
                 match component {
                     std::path::Component::ParentDir => {
                         acc.pop();
@@ -944,8 +944,7 @@ impl Repository {
                     _ => acc.push(component),
                 }
                 acc
-            },
-        );
+            });
         normalized.starts_with(&self.workdir)
     }
 
@@ -1776,6 +1775,8 @@ pub fn from_bare_repository(git_dir: &Path) -> Result<Repository, GitAiError> {
         .to_path_buf();
     let global_args = vec!["-C".to_string(), git_dir.to_string_lossy().to_string()];
 
+    let canonical_workdir = workdir.canonicalize().unwrap_or_else(|_| workdir.clone());
+
     Ok(Repository {
         global_args,
         storage: RepoStorage::for_repo_path(git_dir, &workdir),
@@ -1783,6 +1784,7 @@ pub fn from_bare_repository(git_dir: &Path) -> Result<Repository, GitAiError> {
         pre_command_base_commit: None,
         pre_command_refname: None,
         workdir,
+        canonical_workdir,
     })
 }
 

From 124d8c466dfb06a73ba9b00650f0d58b388152c5 Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 19:13:38 -0500
Subject: [PATCH 14/19] add back snapshots

---
 ...i__authorship__stats__tests__markdown_stats_display.snap | 2 +-
 ...uthorship__stats__tests__markdown_stats_display.snap.new | 6 ------
 tests/snapshots/stats__markdown_stats_all_ai.snap           | 2 +-
 tests/snapshots/stats__markdown_stats_all_human.snap        | 2 +-
 tests/snapshots/stats__markdown_stats_formatting.snap       | 2 +-
 tests/snapshots/stats__markdown_stats_minimal_human.snap    | 2 +-
 tests/snapshots/stats__markdown_stats_mixed.snap            | 2 +-
 tests/snapshots/stats__markdown_stats_no_mixed.snap         | 2 +-
 8 files changed, 7 insertions(+), 13 deletions(-)
 delete mode 100644 src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new

diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap
index 5889e75a..671cb092 100644
--- a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap
+++ b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap
@@ -2,4 +2,4 @@
 source: src/authorship/stats.rs
 expression: mixed_output
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █████████████░░░░░░░  63%\n🤝 mixed  ░░░░░░░░░░░░░██████████  50%\n🤖 ai     ░░░░░░░░░░░░░░██████  31%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 4.0 lines generated for every 1 accepted\n- 1200 mins 9 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █████████████░░░░░░░  63%\n🤝 mixed  ░░░░░░░░░░░░░██████████  50%\n🤖 ai     ░░░░░░░░░░░░░░██████  31%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 4.0 lines generated for every 1 accepted\n- 1200 minutes waiting for AI \n\n</details>"
diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new
deleted file mode 100644
index 91cc02aa..00000000
--- a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display.snap.new
+++ /dev/null
@@ -1,6 +0,0 @@
----
-source: src/authorship/stats.rs
-assertion_line: 768
-expression: mixed_output
----
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █████████████░░░░░░░  63%\n🤝 mixed  ░░░░░░░░░░░░░██████████  50%\n🤖 ai     ░░░░░░░░░░░░░░██████  31%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 4.0 lines generated for every 1 accepted\n- 1200 minutes waiting for AI \n\n</details>"
diff --git a/tests/snapshots/stats__markdown_stats_all_ai.snap b/tests/snapshots/stats__markdown_stats_all_ai.snap
index 6a6d6869..6a543f15 100644
--- a/tests/snapshots/stats__markdown_stats_all_ai.snap
+++ b/tests/snapshots/stats__markdown_stats_all_ai.snap
@@ -2,4 +2,4 @@
 source: tests/stats.rs
 expression: markdown
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ░░░░░░░░░░░░░░░░░░░░  0%\n🤖 ai     ████████████████████  100%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.0 lines generated for every 1 accepted\n- 30 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ░░░░░░░░░░░░░░░░░░░░  0%\n🤖 ai     ████████████████████  100%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.0 lines generated for every 1 accepted\n- 30 seconds waiting for AI \n\n</details>"
diff --git a/tests/snapshots/stats__markdown_stats_all_human.snap b/tests/snapshots/stats__markdown_stats_all_human.snap
index 43a68fe8..a291943a 100644
--- a/tests/snapshots/stats__markdown_stats_all_human.snap
+++ b/tests/snapshots/stats__markdown_stats_all_human.snap
@@ -2,4 +2,4 @@
 source: tests/stats.rs
 expression: markdown
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████████████████  100%\n🤖 ai     ░░░░░░░░░░░░░░░░░░░░  0%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 0.0 lines generated for every 1 accepted\n- 0 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████████████████  100%\n🤖 ai     ░░░░░░░░░░░░░░░░░░░░  0%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 0.0 lines generated for every 1 accepted\n- 0 seconds waiting for AI \n\n</details>"
diff --git a/tests/snapshots/stats__markdown_stats_formatting.snap b/tests/snapshots/stats__markdown_stats_formatting.snap
index 0fce86af..4a6a753f 100644
--- a/tests/snapshots/stats__markdown_stats_formatting.snap
+++ b/tests/snapshots/stats__markdown_stats_formatting.snap
@@ -2,4 +2,4 @@
 source: tests/stats.rs
 expression: markdown
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████░░░░░░░░░░░░  38%\n🤝 mixed  ░░░░░░░░███░░░░░░░░░  15%\n🤖 ai     ░░░░░░░░░░░█████████  46%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.7 lines generated for every 1 accepted\n- 25 secs time waiting for AI\n- Top model: cursor::claude-3.5-sonnet (6 accepted lines, 10 generated lines)\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████░░░░░░░░░░░░  38%\n🤝 mixed  ░░░░░░░░███░░░░░░░░░  15%\n🤖 ai     ░░░░░░░░░░░█████████  46%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.7 lines generated for every 1 accepted\n- 25 seconds waiting for AI \n- Top model: cursor::claude-3.5-sonnet (6 accepted lines, 10 generated lines)\n\n</details>"
diff --git a/tests/snapshots/stats__markdown_stats_minimal_human.snap b/tests/snapshots/stats__markdown_stats_minimal_human.snap
index 0b893871..2bd81976 100644
--- a/tests/snapshots/stats__markdown_stats_minimal_human.snap
+++ b/tests/snapshots/stats__markdown_stats_minimal_human.snap
@@ -2,4 +2,4 @@
 source: tests/stats.rs
 expression: markdown
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █░░░░░░░░░░░░░░░░░░░  2%\n🤖 ai     ████████████████████  98%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.0 lines generated for every 1 accepted\n- 10 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █░░░░░░░░░░░░░░░░░░░  2%\n🤖 ai     ████████████████████  98%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.0 lines generated for every 1 accepted\n- 10 seconds waiting for AI \n\n</details>"
diff --git a/tests/snapshots/stats__markdown_stats_mixed.snap b/tests/snapshots/stats__markdown_stats_mixed.snap
index 4599a631..e6e36be3 100644
--- a/tests/snapshots/stats__markdown_stats_mixed.snap
+++ b/tests/snapshots/stats__markdown_stats_mixed.snap
@@ -2,4 +2,4 @@
 source: tests/stats.rs
 expression: markdown
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ███████░░░░░░░░░░░░░  33%\n🤝 mixed  ░░░░░░░███░░░░░░░░░░  17%\n🤖 ai     ░░░░░░░░░░██████████  50%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.7 lines generated for every 1 accepted\n- 45 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ███████░░░░░░░░░░░░░  33%\n🤝 mixed  ░░░░░░░███░░░░░░░░░░  17%\n🤖 ai     ░░░░░░░░░░██████████  50%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.7 lines generated for every 1 accepted\n- 45 seconds waiting for AI \n\n</details>"
diff --git a/tests/snapshots/stats__markdown_stats_no_mixed.snap b/tests/snapshots/stats__markdown_stats_no_mixed.snap
index 0d44dec0..880da7b1 100644
--- a/tests/snapshots/stats__markdown_stats_no_mixed.snap
+++ b/tests/snapshots/stats__markdown_stats_no_mixed.snap
@@ -2,4 +2,4 @@
 source: tests/stats.rs
 expression: markdown
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████░░░░░░░░░░░░  40%\n🤖 ai     ░░░░░░░░████████████  60%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.0 lines generated for every 1 accepted\n- 15 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████░░░░░░░░░░░░  40%\n🤖 ai     ░░░░░░░░████████████  60%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.0 lines generated for every 1 accepted\n- 15 seconds waiting for AI \n\n</details>"

From 5f9a56d28ec400b154187ce8d034351c82c18d73 Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 20:18:28 -0500
Subject: [PATCH 15/19] fix stats

---
 ..._authorship__stats__tests__markdown_stats_display-2.snap | 2 +-
 ...horship__stats__tests__markdown_stats_display-3.snap.new | 6 ++++++
 ...horship__stats__tests__markdown_stats_display-4.snap.new | 6 ++++++
 3 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new
 create mode 100644 src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new

diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-2.snap b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-2.snap
index 4413ab4a..89ba6ac2 100644
--- a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-2.snap
+++ b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-2.snap
@@ -2,4 +2,4 @@
 source: src/authorship/stats.rs
 expression: ai_only_output
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ░░░░░░░░░░░░░░░░░░░░  0%\n🤖 ai     ░███████████████████  95%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.1 lines generated for every 1 accepted\n- 45 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ░░░░░░░░░░░░░░░░░░░░  0%\n🤖 ai     ░███████████████████  95%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.1 lines generated for every 1 accepted\n- 45 seconds waiting for AI \n\n</details>"
diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new
new file mode 100644
index 00000000..3589f2e5
--- /dev/null
+++ b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new
@@ -0,0 +1,6 @@
+---
+source: src/authorship/stats.rs
+assertion_line: 802
+expression: human_only_output
+---
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████████████████  100%\n🤖 ai     ░░░░░░░░░░░░░░░░░░░░  0%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 0.0 lines generated for every 1 accepted\n- 0 seconds waiting for AI \n\n</details>"
diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new
new file mode 100644
index 00000000..b40943d3
--- /dev/null
+++ b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new
@@ -0,0 +1,6 @@
+---
+source: src/authorship/stats.rs
+assertion_line: 819
+expression: minimal_human_output
+---
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █░░░░░░░░░░░░░░░░░░░  2%\n🤖 ai     ░███████████████████  93%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.1 lines generated for every 1 accepted\n- 30 seconds waiting for AI \n\n</details>"

From fc4fc982c61866fc7517526144f3d9ce1ce2c519 Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 20:19:49 -0500
Subject: [PATCH 16/19] fix other tests

---
 ..._authorship__stats__tests__markdown_stats_display-3.snap | 2 +-
 ...horship__stats__tests__markdown_stats_display-3.snap.new | 6 ------
 ..._authorship__stats__tests__markdown_stats_display-4.snap | 2 +-
 ...horship__stats__tests__markdown_stats_display-4.snap.new | 6 ------
 4 files changed, 2 insertions(+), 14 deletions(-)
 delete mode 100644 src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new
 delete mode 100644 src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new

diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap
index a42a3e75..4b379051 100644
--- a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap
+++ b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap
@@ -2,4 +2,4 @@
 source: src/authorship/stats.rs
 expression: human_only_output
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████████████████  100%\n🤖 ai     ░░░░░░░░░░░░░░░░░░░░  0%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 0.0 lines generated for every 1 accepted\n- 0 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████████████████  100%\n🤖 ai     ░░░░░░░░░░░░░░░░░░░░  0%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 0.0 lines generated for every 1 accepted\n- 0 seconds waiting for AI \n\n</details>"
diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new
deleted file mode 100644
index 3589f2e5..00000000
--- a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-3.snap.new
+++ /dev/null
@@ -1,6 +0,0 @@
----
-source: src/authorship/stats.rs
-assertion_line: 802
-expression: human_only_output
----
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    ████████████████████  100%\n🤖 ai     ░░░░░░░░░░░░░░░░░░░░  0%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 0.0 lines generated for every 1 accepted\n- 0 seconds waiting for AI \n\n</details>"
diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap
index eee72b8e..a000284e 100644
--- a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap
+++ b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap
@@ -2,4 +2,4 @@
 source: src/authorship/stats.rs
 expression: minimal_human_output
 ---
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █░░░░░░░░░░░░░░░░░░░  2%\n🤖 ai     ░███████████████████  93%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.1 lines generated for every 1 accepted\n- 30 secs time waiting for AI\n\n</details>"
+"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █░░░░░░░░░░░░░░░░░░░  2%\n🤖 ai     ░███████████████████  93%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.1 lines generated for every 1 accepted\n- 30 seconds waiting for AI \n\n</details>"
diff --git a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new b/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new
deleted file mode 100644
index b40943d3..00000000
--- a/src/authorship/snapshots/git_ai__authorship__stats__tests__markdown_stats_display-4.snap.new
+++ /dev/null
@@ -1,6 +0,0 @@
----
-source: src/authorship/stats.rs
-assertion_line: 819
-expression: minimal_human_output
----
-"Stats powered by [Git AI](https://github.com/acunniffe/git-ai)\n\n```text\n🧠 you    █░░░░░░░░░░░░░░░░░░░  2%\n🤖 ai     ░███████████████████  93%\n```\n\n<details>\n<summary>More stats</summary>\n\n- 1.1 lines generated for every 1 accepted\n- 30 seconds waiting for AI \n\n</details>"

From 1aa52fb5e6df1b51eac7f160d0378229b38c483b Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 20:27:52 -0500
Subject: [PATCH 17/19] revert back to unix file executable

---
 scripts/dev-symlinks.sh                    | 0
 tests/git-compat/run.py                    | 0
 tests/github/scripts/cleanup-test-repos.sh | 0
 tests/github/scripts/run-github-tests.sh   | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 scripts/dev-symlinks.sh
 mode change 100644 => 100755 tests/git-compat/run.py
 mode change 100644 => 100755 tests/github/scripts/cleanup-test-repos.sh
 mode change 100644 => 100755 tests/github/scripts/run-github-tests.sh

diff --git a/scripts/dev-symlinks.sh b/scripts/dev-symlinks.sh
old mode 100644
new mode 100755
diff --git a/tests/git-compat/run.py b/tests/git-compat/run.py
old mode 100644
new mode 100755
diff --git a/tests/github/scripts/cleanup-test-repos.sh b/tests/github/scripts/cleanup-test-repos.sh
old mode 100644
new mode 100755
diff --git a/tests/github/scripts/run-github-tests.sh b/tests/github/scripts/run-github-tests.sh
old mode 100644
new mode 100755

From 954822d21adf5fb2ccc375699cdbb1e67cd570cb Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 20:36:05 -0500
Subject: [PATCH 18/19] remove loggers

---
 src/authorship/rebase_authorship.rs |  7 -------
 src/commands/checkpoint.rs          | 21 +++++++++----------
 src/commands/git_ai_handlers.rs     |  3 ---
 src/git/repo_storage.rs             |  4 ----
 tests/ai_tab.rs                     | 32 +++++++++++++----------------
 tests/repos/test_file.rs            |  8 +++-----
 tests/repos/test_repo.rs            |  6 ++++--
 7 files changed, 31 insertions(+), 50 deletions(-)

diff --git a/src/authorship/rebase_authorship.rs b/src/authorship/rebase_authorship.rs
index ec63da4c..8465ef62 100644
--- a/src/authorship/rebase_authorship.rs
+++ b/src/authorship/rebase_authorship.rs
@@ -703,14 +703,10 @@ pub fn rewrite_authorship_after_commit_amend(
     let changed_files = repo.list_commit_files(amended_commit, None)?;
     let mut pathspecs: HashSet<String> = changed_files.into_iter().collect();
 
-    // println!("changed_files: {:?}", changed_files);
-
     let working_log = repo.storage.working_log_for_base_commit(original_commit);
     let touched_files = working_log.all_touched_files()?;
     pathspecs.extend(touched_files);
 
-    println!("pathspecs: {:?}", pathspecs);
-
     // Check if original commit has an authorship log with prompts
     let has_existing_log = get_reference_as_authorship_log_v3(repo, original_commit).is_ok();
     let has_existing_prompts = if has_existing_log {
@@ -757,9 +753,6 @@ pub fn rewrite_authorship_after_commit_amend(
             Some(&pathspecs_set),
         )?;
 
-
-    println!("authorship_log: {:?}", authorship_log);
-    println!("initial_attributions: {:?}", initial_attributions);
     // Update base commit SHA
     authorship_log.metadata.base_commit_sha = amended_commit.to_string();
 
diff --git a/src/commands/checkpoint.rs b/src/commands/checkpoint.rs
index 5614968a..2ba7390d 100644
--- a/src/commands/checkpoint.rs
+++ b/src/commands/checkpoint.rs
@@ -24,8 +24,6 @@ pub fn run(
     agent_run_result: Option<AgentRunResult>,
     is_pre_commit: bool,
 ) -> Result<(usize, usize, usize), GitAiError> {
-
-
     // Robustly handle zero-commit repos
     let base_commit = match repo.head() {
         Ok(head) => match head.target() {
@@ -75,7 +73,7 @@ pub fn run(
 
         paths.and_then(|p| {
             let repo_workdir = repo.workdir().ok()?;
-            
+
             let filtered: Vec<String> = p
                 .iter()
                 .filter_map(|path| {
@@ -86,7 +84,7 @@ pub fn run(
                         // Relative path - join with workdir
                         repo_workdir.join(path)
                     };
-                    
+
                     // Use centralized path comparison (handles Windows canonical paths correctly)
                     if repo.path_is_in_workdir(&path_buf) {
                         // Convert to relative path for git operations
@@ -98,7 +96,9 @@ pub fn run(
                                 // Fallback: try with canonical paths
                                 let canonical_workdir = repo_workdir.canonicalize().ok()?;
                                 let canonical_path = path_buf.canonicalize().ok()?;
-                                if let Ok(relative) = canonical_path.strip_prefix(&canonical_workdir) {
+                                if let Ok(relative) =
+                                    canonical_path.strip_prefix(&canonical_workdir)
+                                {
                                     // Normalize path separators to forward slashes for git
                                     Some(normalize_to_posix(&relative.to_string_lossy()))
                                 } else {
@@ -124,8 +124,6 @@ pub fn run(
         })
     });
 
-
-    println!("pathspec_filter: {:?}", pathspec_filter);
     let files = get_all_tracked_files(
         repo,
         &base_commit,
@@ -134,8 +132,6 @@ pub fn run(
         is_pre_commit,
     )?;
 
-    println!("files: {:?}", files);
-
     let mut checkpoints = if reset {
         // If reset flag is set, start with an empty working log
         working_log.reset_working_log()?;
@@ -463,7 +459,9 @@ fn get_checkpoint_entry_for_file(
     initial_attributions: Arc<HashMap<String, Vec<LineAttribution>>>,
     ts: u128,
 ) -> Result<Option<WorkingLogEntry>, GitAiError> {
-    let current_content = working_log.read_current_file_content(&file_path).unwrap_or_default();
+    let current_content = working_log
+        .read_current_file_content(&file_path)
+        .unwrap_or_default();
 
     // Try to get previous state from checkpoints first
     let from_checkpoint = previous_checkpoints.iter().rev().find_map(|checkpoint| {
@@ -1256,7 +1254,8 @@ fn is_text_file(working_log: &PersistedWorkingLog, path: &str) -> bool {
         .unwrap_or(false);
 
     if !skip_metadata_check {
-        if let Ok(metadata) = std::fs::metadata(working_log.to_repo_absolute_path(&normalized_path)) {
+        if let Ok(metadata) = std::fs::metadata(working_log.to_repo_absolute_path(&normalized_path))
+        {
             if !metadata.is_file() {
                 return false;
             }
diff --git a/src/commands/git_ai_handlers.rs b/src/commands/git_ai_handlers.rs
index 45826d9a..14905987 100644
--- a/src/commands/git_ai_handlers.rs
+++ b/src/commands/git_ai_handlers.rs
@@ -332,9 +332,6 @@ fn handle_checkpoint(args: &[String]) {
         .map(|r| r.checkpoint_kind)
         .unwrap_or(CheckpointKind::Human);
 
-    println!("checkpoint_kind: {:?}", checkpoint_kind);
-    println!("files for mock_ai: {:?}", get_all_files_for_mock_ai(&final_working_dir));
-
     if CheckpointKind::Human == checkpoint_kind && agent_run_result.is_none() {
         println!(
             "get_all_files_for_mock_ai HUMAN Checkpoints: {:?}",
diff --git a/src/git/repo_storage.rs b/src/git/repo_storage.rs
index 355ac7a4..d83f6687 100644
--- a/src/git/repo_storage.rs
+++ b/src/git/repo_storage.rs
@@ -157,8 +157,6 @@ impl PersistedWorkingLog {
     }
 
     pub fn set_dirty_files(&mut self, dirty_files: Option<HashMap<String, String>>) {
-        println!("pre_transform dirty_files: {:?}", dirty_files);
-
         let normalized_dirty_files = dirty_files.map(|map| {
             map.into_iter()
                 .map(|(file_path, content)| {
@@ -170,8 +168,6 @@ impl PersistedWorkingLog {
         });
 
         self.dirty_files = normalized_dirty_files;
-
-        println!("setdirty_files: {:?}", self.dirty_files);
     }
 
     pub fn reset_working_log(&self) -> Result<(), GitAiError> {
diff --git a/tests/ai_tab.rs b/tests/ai_tab.rs
index 9aae3987..0ec6637e 100644
--- a/tests/ai_tab.rs
+++ b/tests/ai_tab.rs
@@ -135,10 +135,7 @@ fn test_ai_tab_after_edit_checkpoint_includes_dirty_files_and_paths() {
     let edited = result
         .edited_filepaths
         .expect("after_edit should include edited filepaths");
-    assert_eq!(
-        edited,
-        vec!["/Users/test/project/src/main.rs".to_string()]
-    );
+    assert_eq!(edited, vec!["/Users/test/project/src/main.rs".to_string()]);
 
     let dirty_files = result
         .dirty_files
@@ -173,7 +170,10 @@ fn test_ai_tab_rejects_invalid_hook_event() {
                 message
             );
         }
-        other => panic!("expected PresetError for invalid hook_event_name, got {:?}", other),
+        other => panic!(
+            "expected PresetError for invalid hook_event_name, got {:?}",
+            other
+        ),
     }
 }
 
@@ -252,7 +252,9 @@ fn test_ai_tab_e2e_marks_ai_lines() {
     );
 
     // AI tab inserts new lines alongside the existing content
-    let ai_content = "console.log(\"hello world\");\n// Log hello world\nconsole.log(\"hello from ai\");\n".to_string();
+    let ai_content =
+        "console.log(\"hello world\");\n// Log hello world\nconsole.log(\"hello from ai\");\n"
+            .to_string();
     fs::write(&file_path, &ai_content).unwrap();
 
     run_ai_tab_checkpoint(
@@ -269,7 +271,8 @@ fn test_ai_tab_e2e_marks_ai_lines() {
         }),
     );
 
-    repo.stage_all_and_commit("Accept AI tab completion").unwrap();
+    repo.stage_all_and_commit("Accept AI tab completion")
+        .unwrap();
 
     let mut file = repo.filename(relative_path);
     file.assert_lines_and_blame(lines![
@@ -304,11 +307,7 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
     let lib_file_path_str = lib_file_path.to_string_lossy().to_string();
     let readme_file_path_str = readme_file_path.to_string_lossy().to_string();
 
-    println!("lib_file_path_str: {}", lib_file_path_str);
-    println!("readme_file_path_str: {}", readme_file_path_str);
-
     let working_logs = repo.current_working_logs();
-    println!("dirty_files: {:?}", working_logs.dirty_files);
 
     // Before edit snapshot includes all dirty files (AI target plus unrelated human edits)
     run_ai_tab_checkpoint(
@@ -333,7 +332,6 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
     fs::write(&lib_file_path, &ai_content).unwrap();
 
     let working_logs = repo.current_working_logs();
-    println!("dirty_files: {:?}", working_logs.dirty_files);
 
     run_ai_tab_checkpoint(
         &repo,
@@ -350,13 +348,11 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         }),
     );
 
-
     let working_logs = repo.current_working_logs();
-    println!("dirty_files: {:?}", working_logs.dirty_files);
-
-    let commit_result = repo.stage_all_and_commit("Record AI tab completion while other files dirty").unwrap();
-    println!("COMMIT OUTPUT: {}", commit_result.stdout);
 
+    let commit_result = repo
+        .stage_all_and_commit("Record AI tab completion while other files dirty")
+        .unwrap();
 
     commit_result.print_authorship();
 
@@ -369,4 +365,4 @@ fn test_ai_tab_e2e_handles_dirty_files_map() {
         "    println!(\"from ai\");".ai(),
         "}".ai(),
     ]);
-}
\ No newline at end of file
+}
diff --git a/tests/repos/test_file.rs b/tests/repos/test_file.rs
index f0de88de..994a41ee 100644
--- a/tests/repos/test_file.rs
+++ b/tests/repos/test_file.rs
@@ -727,12 +727,10 @@ impl<'a> TestFile<'a> {
     fn write_and_checkpoint(&self, author_type: &AuthorType) {
         let contents = self.contents();
         fs::write(&self.file_path, contents).unwrap();
-        let _ = if author_type == &AuthorType::Ai {
-            let a = self.repo.git_ai(&["checkpoint", "mock_ai"]);
-            println!("checkpoint result: {:?}", a);
-            a
+        if author_type == &AuthorType::Ai {
+            self.repo.git_ai(&["checkpoint", "mock_ai"]).unwrap();
         } else {
-            self.repo.git_ai(&["checkpoint"])
+            self.repo.git_ai(&["checkpoint"]).unwrap();
         };
     }
 
diff --git a/tests/repos/test_repo.rs b/tests/repos/test_repo.rs
index da6798de..7df7d361 100644
--- a/tests/repos/test_repo.rs
+++ b/tests/repos/test_repo.rs
@@ -40,7 +40,9 @@ impl TestRepo {
     }
 
     pub fn canonical_path(&self) -> PathBuf {
-        self.path.canonicalize().expect("failed to canonicalize test repo path")
+        self.path
+            .canonicalize()
+            .expect("failed to canonicalize test repo path")
     }
 
     pub fn stats(&self) -> Result<CommitStats, String> {
@@ -228,7 +230,7 @@ impl TestRepo {
 
 impl Drop for TestRepo {
     fn drop(&mut self) {
-        // fs::remove_dir_all(self.path.clone()).expect("failed to remove test repo");
+        fs::remove_dir_all(self.path.clone()).expect("failed to remove test repo");
     }
 }
 

From 1e755c640030c1ff10dadcc86be2494e1765314f Mon Sep 17 00:00:00 2001
From: Aidan Cunniffe <acunniffe@gmail.com>
Date: Mon, 10 Nov 2025 20:56:55 -0500
Subject: [PATCH 19/19] parallel tests

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4bb6911d..0e21cdad 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -40,6 +40,6 @@ jobs:
             ${{ runner.os }}-cargo-
 
       - name: Run tests
-        run: cargo test -- --test-threads=1
+        run: cargo test
         env:
           CARGO_INCREMENTAL: 0