chore: Create zizmor.yml

.beads/.gitignore

@@ -1,52 +1,51 @@
-# SQLite databases
-*.db
-*.db?*
-*.db-journal
-*.db-wal
-*.db-shm
-*.sqlite3
+# Dolt database (managed by Dolt, not git)
+dolt/
+dolt-access.lock
 
-# Daemon runtime files
-daemon.lock
-daemon.log
-daemon-*.log.gz
-daemon.pid
+# Runtime files
 bd.sock
+bd.sock.startlock
 sync-state.json
 last-touched
 
 # Local version tracking (prevents upgrade notification spam after git ops)
 .local_version
 
-# Legacy database files
-db.sqlite
-bd.db
-
 # Worktree redirect file (contains relative path to main repo's .beads/)
 # Must not be committed as paths would be wrong in other clones
 redirect
 
-# Merge artifacts (temporary files from 3-way merge)
-beads.base.jsonl
-beads.base.meta.json
-beads.left.jsonl
-beads.left.meta.json
-beads.right.jsonl
-beads.right.meta.json
-
 # Sync state (local-only, per-machine)
 # These files are machine-specific and should not be shared across clones
 .sync.lock
-.jsonl.lock
-sync_base.jsonl
 export-state/
 
-# Dolt database (managed by Dolt remotes, not git)
-dolt/
-dolt-access.lock
+# Ephemeral store (SQLite - wisps/molecules, intentionally not versioned)
+ephemeral.sqlite3
+ephemeral.sqlite3-journal
+ephemeral.sqlite3-wal
+ephemeral.sqlite3-shm
+
+# Dolt server management (auto-started by bd)
+dolt-server.pid
+dolt-server.log
+dolt-server.lock
+dolt-server.port
+dolt-server.activity
+dolt-monitor.pid
 
-# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here.
-# They would override fork protection in .git/info/exclude, allowing
-# contributors to accidentally commit upstream issue databases.
-# The JSONL files (issues.jsonl, interactions.jsonl) and config files
-# are tracked by git by default since no pattern above ignores them.
+# Backup data (auto-exported JSONL, local-only)
+backup/
+
+# Legacy files (from pre-Dolt versions)
+*.db
+*.db?*
+*.db-journal
+*.db-wal
+*.db-shm
+db.sqlite
+bd.db
+# NOTE: Do NOT add negation patterns here.
+# They would override fork protection in .git/info/exclude.
+# Config files (metadata.json, config.yaml) are tracked by git by default
+# since no pattern above ignores them.

.beads/backup/backup_state.json

@@ -0,0 +1,13 @@
+{
+  "last_dolt_commit": "fit9rrh4oo30fkpqacfa5i999p582hrc",
+  "last_event_id": 0,
+  "timestamp": "2026-03-06T07:05:13.345572Z",
+  "counts": {
+    "issues": 111,
+    "events": 0,
+    "comments": 0,
+    "dependencies": 14,
+    "labels": 4,
+    "config": 13
+  }
+}

.beads/backup/config.jsonl

@@ -0,0 +1,13 @@
+{"key":"auto_compact_enabled","value":"false"}
+{"key":"compact_batch_size","value":"50"}
+{"key":"compact_model","value":"claude-haiku-4-5-20251001"}
+{"key":"compact_parallel_workers","value":"5"}
+{"key":"compact_tier1_days","value":"30"}
+{"key":"compact_tier1_dep_levels","value":"2"}
+{"key":"compact_tier2_commits","value":"100"}
+{"key":"compact_tier2_days","value":"90"}
+{"key":"compact_tier2_dep_levels","value":"5"}
+{"key":"compaction_enabled","value":"false"}
+{"key":"issue_prefix","value":"el"}
+{"key":"schema_version","value":"6"}
+{"key":"types.custom","value":"molecule,gate,convoy,merge-request,slot,agent,role,rig,message"}

.beads/backup/dependencies.jsonl

@@ -0,0 +1,14 @@
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-713","issue_id":"el-713.1","type":"parent-child"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-713","issue_id":"el-713.2","type":"parent-child"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-713","issue_id":"el-713.3","type":"parent-child"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-713","issue_id":"el-713.4","type":"parent-child"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-713","issue_id":"el-713.5","type":"parent-child"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-713","issue_id":"el-713.6","type":"parent-child"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-6yg","issue_id":"el-8wn","type":"blocks"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-oxv","issue_id":"el-8wn","type":"blocks"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-6yg","issue_id":"el-dcb","type":"blocks"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-oxv","issue_id":"el-dcb","type":"blocks"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-5mr","issue_id":"el-e9r","type":"blocks"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-ffc","issue_id":"el-ffc.1","type":"parent-child"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-5mr","issue_id":"el-gwo","type":"blocks"}
+{"created_at":"2026-02-16T15:38:03Z","created_by":"import","depends_on_id":"el-5mr","issue_id":"el-pre","type":"blocks"}

.beads/backup/labels.jsonl

@@ -0,0 +1,4 @@
+{"issue_id":"el-ffc","label":"status:in-progress"}
+{"issue_id":"el-yr6","label":"security"}
+{"issue_id":"el-yr6","label":"testing"}
+{"issue_id":"el-yr6","label":"tests"}

.github/dependabot.yml

@@ -15,6 +15,7 @@ updates:
       semver-major-days: 10
       semver-minor-days: 5
       semver-patch-days: 2
+      default-days: 7
   # Enable version checks and updates for Rust dependencies.
   - package-ecosystem: "cargo"
     directory: "/native/ecto_libsql/"
@@ -25,6 +26,7 @@ updates:
       semver-major-days: 10
       semver-minor-days: 5
       semver-patch-days: 2
+      default-days: 7
   # Enable version updates for GitHub Actions.
   - package-ecosystem: "github-actions"
     # Workflow files stored in the default location of `.github/workflows`
@@ -33,3 +35,5 @@ updates:
     schedule:
       interval: "monthly"
     target-branch: "dev"
+    cooldown:
+      default-days: 7