feat: add transition, link, array ops, and bulk set commands

.agents/skills/beads/SKILL.md

@@ -0,0 +1,80 @@
+---
+name: beads
+description: Use when working in a repository that uses bd or Beads for durable project task tracking, issue dependencies, blocker management, multi-session handoff, or shared work memory. Trigger when the user asks to find ready work, claim or close tasks, create follow-up work, inspect blockers, recover project context, or choose between local planning and persistent project tracking.
+---
+
+# Beads
+
+Use Beads as the shared project task system. Local plans, scratch files, and personal memories are useful, but they are not the durable source of truth for project work.
+
+## First Step
+
+Run:
+
+```bash
+bd prime
+```
+
+If that prints nothing, check whether the repository has an active Beads workspace:
+
+```bash
+bd where
+```
+
+## Preferred Route
+
+Use the `bd` CLI when shell access is available. It is the most compact and direct Beads interface.
+
+## Core CLI Workflow
+
+1. Find work:
+
+```bash
+bd ready
+bd list --status=open
+bd list --status=in_progress
+```
+
+2. Inspect before editing:
+
+```bash
+bd show <id>
+```
+
+3. Claim work atomically:
+
+```bash
+bd update <id> --claim
+```
+
+4. Create durable follow-up work when implementation reveals new tasks:
+
+```bash
+bd create "Short title" --description="Why this exists and what needs to be done" --type=task --priority=2
+```
+
+5. Close completed work:
+
+```bash
+bd close <id> --reason="Completed"
+```
+
+## What Belongs In Beads
+
+Use Beads for:
+
+- shared project tasks
+- blockers and dependencies
+- discovered follow-up work
+- work that must survive thread reset, compaction, or handoff
+- status that another person or agent should be able to resume
+
+Use agent-local planning tools only for the current turn's execution checklist. Do not treat them as shared project state.
+
+## Rules
+
+- Do not create markdown TODO files as the source of truth when Beads is available.
+- Do not use `bd edit`; it opens an interactive editor. Use `bd update` flags instead.
+- Prefer `--json` when parsing `bd` output programmatically.
+- If hooks are installed, `bd prime` may already be injected. Run it manually when context is missing.
+- Do not auto-close or mutate tasks unless the work is actually complete.

.agents/skills/beads/agents/openai.yaml

@@ -0,0 +1,4 @@
+interface:
+  display_name: "Beads"
+  short_description: "Project task tracking with bd"
+  default_prompt: "Use $beads to inspect ready work and manage durable project tasks."

.beads/.gitignore

@@ -1,16 +1,32 @@
 # Dolt database (managed by Dolt, not git)
 dolt/
-dolt-access.lock
+embeddeddolt/
+proxieddb/
 
 # Runtime files
 bd.sock
 bd.sock.startlock
 sync-state.json
 last-touched
+.exclusive-lock
+
+# Daemon runtime (lock, log, pid)
+daemon.*
+
+# Push state (runtime, per-machine)
+push-state.json
+
+# Lock files (various runtime locks)
+*.lock
+
+# Credential key (encryption key for federation peer auth — never commit)
+.beads-credential-key
 
 # Local version tracking (prevents upgrade notification spam after git ops)
 .local_version
 
+proxied_server_client_info.json
+
 # Worktree redirect file (contains relative path to main repo's .beads/)
 # Must not be committed as paths would be wrong in other clones
 redirect
@@ -19,6 +35,7 @@ redirect
 # These files are machine-specific and should not be shared across clones
 .sync.lock
 export-state/
+export-state.json
 
 # Ephemeral store (SQLite - wisps/molecules, intentionally not versioned)
 ephemeral.sqlite3
@@ -31,10 +48,20 @@ dolt-server.pid
 dolt-server.log
 dolt-server.lock
 dolt-server.port
+dolt-server.activity
+
+# Debug-mode pprof artifacts (written when dolt.debug: true in config.yaml)
+dolt-pprof/
+
+# Corrupt backup directories (created by bd doctor --fix recovery)
+*.corrupt.backup/
 
 # Backup data (auto-exported JSONL, local-only)
 backup/
 
+# Per-project environment file (Dolt connection config, GH#2520)
+.env
+
 # Legacy files (from pre-Dolt versions)
 *.db
 *.db?*

.beads/README.md

@@ -36,7 +36,7 @@ Issues in Beads are:
 - **Git-native**: Stored in Dolt database with version control and branching
 - **AI-friendly**: CLI-first design works perfectly with AI coding agents
 - **Branch-aware**: Issues can follow your branch workflow
-- **Always in sync**: Auto-syncs with your commits
+- **Sync-ready**: Uses Dolt remotes for backup and team sharing
 
 ## Why Beads?
 
@@ -51,7 +51,7 @@ Issues in Beads are:
 - Fast, lightweight, and stays out of your way
 
 🔧 **Git Integration**
-- Automatic sync with git commits
+- Dolt-native sync via bd dolt push / bd dolt pull
 - Branch-aware issue tracking
 - Dolt-native three-way merge resolution
 

.beads/config.yaml

@@ -1 +1,68 @@
-no-db: true
+# Beads Configuration File
+# This file configures default behavior for all bd commands in this repository
+# All settings can also be set via environment variables (BD_* prefix)
+# or overridden with command-line flags
+
+# Issue prefix for this repository (used by bd init)
+# If not set, bd init will auto-detect from directory name
+# Example: issue-prefix: "myproject" creates issues like "myproject-1", "myproject-2", etc.
+# issue-prefix: ""
+
+# Use no-db mode: JSONL-only, no Dolt database
+# When true, .beads/issues.jsonl is the only local store
+# no-db: false
+
+# Enable JSON output by default
+# json: false
+
+# Feedback title formatting for mutating commands (create/update/close/dep/edit)
+# 0 = hide titles, N > 0 = truncate to N characters
+# output:
+#   title-length: 255
+
+# Default actor for audit trails (overridden by BEADS_ACTOR or --actor)
+# actor: ""
+
+# Export events (audit trail) to .beads/events.jsonl on each flush/sync
+# When enabled, new events are appended incrementally using a high-water mark.
+# Use 'bd export --events' to trigger manually regardless of this setting.
+# events-export: false
+
+# Multi-repo configuration (experimental - bd-307)
+# Allows hydrating from multiple repositories and routing writes to the correct database
+# repos:
+#   primary: "."  # Primary repo (where this database lives)
+#   additional:   # Additional repos to hydrate from (read-only)
+#     - ~/beads-planning  # Personal planning repo
+#     - ~/work-planning   # Work planning repo
+
+# Dolt-native backup (periodic backup for off-machine recovery)
+# This is full database backup only. Cross-machine sync uses Dolt remotes.
+# backup:
+#   enabled: false     # Disable auto-backup entirely
+#   interval: 15m      # Minimum time between auto-backups
+#   git-push: false    # Disable git push (backup locally only)
+#   git-repo: ""       # Separate git repo for backups (default: project repo)
+
+# Optional JSONL auto-export for viewers, interchange, and issue-level migration.
+# Disabled by default; enable only when an integration needs fresh .beads/issues.jsonl.
+# Use relative paths under .beads/ for JSONL import/export filenames.
+# export:
+#   auto: false
+#   path: issues.jsonl
+#   interval: 60s
+#   git-add: false
+# import:
+#   path: issues.jsonl
+
+# Integration settings (access with 'bd config get/set')
+# Non-secret keys (stored in the database):
+# - jira.url, jira.project
+# - linear.team_id
+# - github.org, github.repo
+#
+# Secret keys (stored in this file but prefer env vars to avoid git exposure):
+# - linear.api_key  → use LINEAR_API_KEY env var instead
+# - github.token    → use GITHUB_TOKEN env var instead
+
+sync.remote: "git+ssh://git@github.com/sthadka/jai.git"

.beads/hooks/post-checkout

@@ -1,24 +1,33 @@
 #!/usr/bin/env sh
-# --- BEGIN BEADS INTEGRATION v0.60.0 ---
+# --- BEGIN BEADS INTEGRATION v1.0.5 ---
 # This section is managed by beads. Do not remove these markers.
 if command -v bd >/dev/null 2>&1; then
   export BD_GIT_HOOK=1
-  _bd_timeout=${BEADS_HOOK_TIMEOUT:-30}
+  _bd_timeout=${BEADS_HOOK_TIMEOUT:-300}
+  _bd_used_perl=0
   if command -v timeout >/dev/null 2>&1; then
     timeout "$_bd_timeout" bd hooks run post-checkout "$@"
     _bd_exit=$?
-    if [ $_bd_exit -eq 124 ]; then
-      echo >&2 "beads: hook 'post-checkout' timed out after ${_bd_timeout}s — continuing without beads"
-      _bd_exit=0
-    fi
+  elif command -v gtimeout >/dev/null 2>&1; then
+    gtimeout "$_bd_timeout" bd hooks run post-checkout "$@"
+    _bd_exit=$?
+  elif command -v perl >/dev/null 2>&1; then
+    _bd_used_perl=1
+    perl -e 'alarm shift; exec @ARGV' "$_bd_timeout" bd hooks run post-checkout "$@"
+    _bd_exit=$?
   else
+    echo >&2 "beads: hook 'post-checkout' running without timeout; install coreutils or perl to enable BEADS_HOOK_TIMEOUT"
     bd hooks run post-checkout "$@"
     _bd_exit=$?
   fi
+  if [ $_bd_exit -eq 124 ] || { [ $_bd_used_perl -eq 1 ] && [ $_bd_exit -eq 142 ]; }; then
+    echo >&2 "beads: hook 'post-checkout' timed out after ${_bd_timeout}s — continuing without beads"
+    _bd_exit=0
+  fi
   if [ $_bd_exit -eq 3 ]; then
     echo >&2 "beads: database not initialized — skipping hook 'post-checkout'"
     _bd_exit=0
   fi
   if [ $_bd_exit -ne 0 ]; then exit $_bd_exit; fi
 fi
-# --- END BEADS INTEGRATION v0.60.0 ---
+# --- END BEADS INTEGRATION v1.0.5 ---

.beads/hooks/post-merge

@@ -1,24 +1,33 @@
 #!/usr/bin/env sh
-# --- BEGIN BEADS INTEGRATION v0.60.0 ---
+# --- BEGIN BEADS INTEGRATION v1.0.5 ---
 # This section is managed by beads. Do not remove these markers.
 if command -v bd >/dev/null 2>&1; then
   export BD_GIT_HOOK=1
-  _bd_timeout=${BEADS_HOOK_TIMEOUT:-30}
+  _bd_timeout=${BEADS_HOOK_TIMEOUT:-300}
+  _bd_used_perl=0
   if command -v timeout >/dev/null 2>&1; then
     timeout "$_bd_timeout" bd hooks run post-merge "$@"
     _bd_exit=$?
-    if [ $_bd_exit -eq 124 ]; then
-      echo >&2 "beads: hook 'post-merge' timed out after ${_bd_timeout}s — continuing without beads"
-      _bd_exit=0
-    fi
+  elif command -v gtimeout >/dev/null 2>&1; then
+    gtimeout "$_bd_timeout" bd hooks run post-merge "$@"
+    _bd_exit=$?
+  elif command -v perl >/dev/null 2>&1; then
+    _bd_used_perl=1
+    perl -e 'alarm shift; exec @ARGV' "$_bd_timeout" bd hooks run post-merge "$@"
+    _bd_exit=$?
   else
+    echo >&2 "beads: hook 'post-merge' running without timeout; install coreutils or perl to enable BEADS_HOOK_TIMEOUT"
     bd hooks run post-merge "$@"
     _bd_exit=$?
   fi
+  if [ $_bd_exit -eq 124 ] || { [ $_bd_used_perl -eq 1 ] && [ $_bd_exit -eq 142 ]; }; then
+    echo >&2 "beads: hook 'post-merge' timed out after ${_bd_timeout}s — continuing without beads"
+    _bd_exit=0
+  fi
   if [ $_bd_exit -eq 3 ]; then
     echo >&2 "beads: database not initialized — skipping hook 'post-merge'"
     _bd_exit=0
   fi
   if [ $_bd_exit -ne 0 ]; then exit $_bd_exit; fi
 fi
-# --- END BEADS INTEGRATION v0.60.0 ---
+# --- END BEADS INTEGRATION v1.0.5 ---

.beads/hooks/pre-commit

@@ -1,24 +1,33 @@
 #!/usr/bin/env sh
-# --- BEGIN BEADS INTEGRATION v0.60.0 ---
+# --- BEGIN BEADS INTEGRATION v1.0.5 ---
 # This section is managed by beads. Do not remove these markers.
 if command -v bd >/dev/null 2>&1; then
   export BD_GIT_HOOK=1
-  _bd_timeout=${BEADS_HOOK_TIMEOUT:-30}
+  _bd_timeout=${BEADS_HOOK_TIMEOUT:-300}
+  _bd_used_perl=0
   if command -v timeout >/dev/null 2>&1; then
     timeout "$_bd_timeout" bd hooks run pre-commit "$@"
     _bd_exit=$?
-    if [ $_bd_exit -eq 124 ]; then
-      echo >&2 "beads: hook 'pre-commit' timed out after ${_bd_timeout}s — continuing without beads"
-      _bd_exit=0
-    fi
+  elif command -v gtimeout >/dev/null 2>&1; then
+    gtimeout "$_bd_timeout" bd hooks run pre-commit "$@"
+    _bd_exit=$?
+  elif command -v perl >/dev/null 2>&1; then
+    _bd_used_perl=1
+    perl -e 'alarm shift; exec @ARGV' "$_bd_timeout" bd hooks run pre-commit "$@"
+    _bd_exit=$?
   else
+    echo >&2 "beads: hook 'pre-commit' running without timeout; install coreutils or perl to enable BEADS_HOOK_TIMEOUT"
     bd hooks run pre-commit "$@"
     _bd_exit=$?
   fi
+  if [ $_bd_exit -eq 124 ] || { [ $_bd_used_perl -eq 1 ] && [ $_bd_exit -eq 142 ]; }; then
+    echo >&2 "beads: hook 'pre-commit' timed out after ${_bd_timeout}s — continuing without beads"
+    _bd_exit=0
+  fi
   if [ $_bd_exit -eq 3 ]; then
     echo >&2 "beads: database not initialized — skipping hook 'pre-commit'"
     _bd_exit=0
   fi
   if [ $_bd_exit -ne 0 ]; then exit $_bd_exit; fi
 fi
-# --- END BEADS INTEGRATION v0.60.0 ---
+# --- END BEADS INTEGRATION v1.0.5 ---