Merge pull request #750 from alan-turing-institute/staging

Release: Phase 4 UX, Phase 4.5 code quality, Phase 5 testing

Author: chrisdburr

.beads/.gitignore

@@ -1,34 +1,54 @@
-# SQLite databases
-*.db
-*.db?*
-*.db-journal
-*.db-wal
-*.db-shm
+# Dolt database (managed by Dolt, not git)
+dolt/
+dolt-access.lock
 
-# Daemon runtime files
-daemon.lock
-daemon.log
-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
+# Worktree redirect file (contains relative path to main repo's .beads/)
+# Must not be committed as paths would be wrong in other clones
+redirect
+
+# 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/
+
+# Ephemeral store (SQLite - wisps/molecules, intentionally not versioned)
+ephemeral.sqlite3
+ephemeral.sqlite3-journal
+ephemeral.sqlite3-wal
+ephemeral.sqlite3-shm
+
+# Legacy files (from pre-Dolt versions)
+*.db
+*.db?*
+*.db-journal
+*.db-wal
+*.db-shm
 db.sqlite
 bd.db
-
-# Merge artifacts (temporary files from 3-way merge)
+daemon.lock
+daemon.log
+daemon-*.log.gz
+daemon.pid
 beads.base.jsonl
 beads.base.meta.json
 beads.left.jsonl
 beads.left.meta.json
 beads.right.jsonl
 beads.right.meta.json
 
-# Keep JSONL exports and config (source of truth for git)
-!issues.jsonl
-!interactions.jsonl
-!metadata.json
-!config.json
+# 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.

.beads/.jsonl.lock

@@ -0,0 +1 @@
+1772197249

.beads/.migration-hint-ts

@@ -1,4 +1,7 @@
 {
-  "database": "beads.db",
-  "jsonl_export": "issues.jsonl"
-}
+  "database": "dolt",
+  "jsonl_export": "issues.jsonl",
+  "backend": "dolt",
+  "dolt_mode": "server",
+  "dolt_database": "beads_AssurancePlatform"
+}

.beads/issues.jsonl

@@ -0,0 +1,17 @@
+version: 2
+updates:
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 10
+    labels:
+      - "dependencies"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+      - "ci"