core: named rows and one home per repeated rule

[samkeen]

Pure refactor, no behavior change. The wide tuple returns in db.rs
(two of them wearing #[allow(clippy::type_complexity)]) become named
row structs — ResourceListing, ResourceDetail, ResourceBacklinkRow,
ResourceEdgeRow, PendingChunk, InboundEdge — and the inbound-edge
queries stop fetching a src_id no consumer ever read. Rules and dances
written more than once now live once: the meta reads behind the
schema stamp and the recorded embedder (meta_value), the
resolve-ref-then-locate opening of every note-addressed façade op
(resolve_ref_to_path), the two copy-pasted halves of graph::neighbors
(collect_neighbors), the fuse-then-resolve tail shared by the two
search entry points (resolve_hits), the mtime stat read
(ingest::unix_mtime), and the dot-hidden vault-membership rule that
lived as three walk predicates plus validator prose
(pathspec::is_hidden). move_note's by_file map drops the src_id it
stored but never read, matching move_resource's shape. b2-embed gets
the same treatment: files_present is THE installed check the loader,
the provision fast path, and the settings picker all share, and
embed_err is the one candle-to-core error map.

Co-Authored-By: Claude Fable 5 noreply@anthropic.com
Claude-Session: https://claude.ai/code/session_01WE6yzYZhgzwrwYpzaYzMs2

Summary by CodeRabbit

• Improvements
  • Improved consistency when handling hidden files and directories across vault operations.
  • Refined search result processing and resource, note, graph, and link operations.
  • Improved reindexing safeguards, progress handling, and error reporting.
  • Centralized model availability checks for more consistent embedding setup.
  • Preserved existing behavior while improving reliability and maintainability across desktop and CLI workflows.

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Review details

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: c00ce780-53c3-4418-8fc8-44819edc9a4c

📥 Commits

Reviewing files that changed from the base of the PR and between 3264a19 and abcc394.

📒 Files selected for processing (1)

• crates/b2-core/src/pathspec.rs

📝 Walkthrough

Walkthrough

The PR refactors CLI and desktop command handling, introduces structured core database records, centralizes path, metadata, timestamp, embedding, locking, and output helpers, and updates consumers across core operations without changing reported behavior.

Changes

Core database and operation refactoring

Layer / File(s)	Summary
Database contracts and shared helpers crates/b2-core/src/db.rs, crates/b2-core/src/pathspec.rs, crates/b2-core/src/ingest.rs, crates/b2-core/src/dirs.rs	Database queries now return named records. Metadata, hidden-path, and modification-time handling use shared helpers.
Core operation consumers crates/b2-core/src/vault.rs, crates/b2-core/src/graph.rs, crates/b2-core/src/search.rs, crates/b2-core/src/mv.rs, crates/b2-core/src/rm.rs, crates/b2-core/tests/write.rs	Vault, graph, search, move, delete, and embedding code consume structured records and shared resolution helpers.

CLI command refactoring

Layer / File(s)	Summary
Command routing and output crates/b2-cli/src/main.rs, crates/b2-cli/Cargo.toml	Command handlers, reindex reporting, JSON serialization, logging setup, vault opening, and error display were extracted or centralized. The CLI now declares its serde dependency.

Desktop and embedding refactoring

Layer / File(s)	Summary
Desktop vault access and state management crates/b2-desktop/src/main.rs, crates/b2-desktop/src/commands.rs, crates/b2-desktop/src/error.rs, crates/b2-desktop/src/stats.rs, crates/b2-desktop/src/watch.rs	Desktop commands use dedicated vault openers. Reindex cleanup and mutex recovery are shared. Statistics writing and error detail formatting are centralized.
Embedding model helpers crates/b2-embed/src/model.rs, crates/b2-embed/src/config.rs, crates/b2-embed/src/provision.rs	Required model-file checks and Candle error conversion use shared helpers.

Estimated code review effort: 4 (Complex) | ~45 minutes

Possibly related PRs

• AlteredCraft/B2#82: Related Vault note-operation refactoring and shared note-reference resolution.
• AlteredCraft/B2#84: Related CLI reindex handling and ingest reporting changes.
• AlteredCraft/B2#86: Related core graph and search API changes.

Suggested reviewers: claude

Poem

A rabbit sorts records in neat little rows,
Shared helpers guide where each pathway goes.
CLI commands hop into place,
Desktop locks yield with grace.
Models check files, embeddings flow—
A tidy burrow, ready to go.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the core refactor by introducing named rows and centralizing repeated logic.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch claude/rust-codebase-refactor-7ot3v1

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Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@crates/b2-core/src/ingest.rs`:
- Around line 1204-1205: Move the pathspec::is_hidden check in
collect_vault_files ahead of the note-classification match so hidden paths are
excluded before the None arm can add them to notes, while preserving recursive
directory and resource handling for visible paths. Add a regression test
covering a dot-prefixed Markdown file and verify it is absent from the collected
vault paths.

In `@crates/b2-core/src/search.rs`:
- Around line 140-151: Update resolve_hits so limit == 0 returns immediately,
then iterate through all fused candidates without applying take(limit) before
resolution; only stop once hits.len() reaches limit, allowing later valid notes
to replace unresolved chunks while preserving ranked order.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: d9a48398-9740-4be1-b50c-16ac1fc60b1f

📥 Commits

Reviewing files that changed from the base of the PR and between fa22460 and 3264a19.

⛔ Files ignored due to path filters (1)

• Cargo.lock is excluded by !**/*.lock

📒 Files selected for processing (20)

• crates/b2-cli/Cargo.toml
• crates/b2-cli/src/main.rs
• crates/b2-core/src/db.rs
• crates/b2-core/src/dirs.rs
• crates/b2-core/src/graph.rs
• crates/b2-core/src/ingest.rs
• crates/b2-core/src/mv.rs
• crates/b2-core/src/pathspec.rs
• crates/b2-core/src/rm.rs
• crates/b2-core/src/search.rs
• crates/b2-core/src/vault.rs
• crates/b2-core/tests/write.rs
• crates/b2-desktop/src/commands.rs
• crates/b2-desktop/src/error.rs
• crates/b2-desktop/src/main.rs
• crates/b2-desktop/src/stats.rs
• crates/b2-desktop/src/watch.rs
• crates/b2-embed/src/config.rs
• crates/b2-embed/src/model.rs
• crates/b2-embed/src/provision.rs