bd init: initialize beads issue tracking

.beads/config.yaml

@@ -64,3 +64,5 @@
 # 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+https://git.darkmark.co.uk/amerlo/nutrition-mcp.git"

.gitignore

@@ -6,3 +6,8 @@
 .env
 # IDE
 .idea/
+
+# Beads / Dolt files (added by bd init)
+.dolt/
+.beads-credential-key
+.beads/proxieddb/

AGENTS.md

@@ -108,4 +108,84 @@ rm -f file                  # NOT: rm file
 2. **Run quality gates** - `cargo build --release && cargo test`
 3. **Close completed issues** - `bd close <id1> <id2> ...`
 4. **PUSH** - `git add -A && git commit -m "..." && git push`
-5. **Verify** - `git status` must show clean working tree
+5. **Verify** - `git status` must show clean working tree
+
+<!-- BEGIN BEADS INTEGRATION v:1 profile:minimal hash:970c3bf2 -->
+## Beads Issue Tracker
+
+This project uses **bd (beads)** for issue tracking. Run `bd prime` to see full workflow context and commands.
+
+### Quick Reference
+
+```bash
+bd ready              # Find available work
+bd show <id>          # View issue details
+bd update <id> --claim  # Claim work
+bd close <id>         # Complete work
+```
+
+### Rules
+
+- Use `bd` for ALL task tracking — do NOT use TodoWrite, TaskCreate, or markdown TODO lists
+- Run `bd prime` for detailed command reference and session close protocol
+- Use `bd remember` for persistent knowledge — do NOT use MEMORY.md files
+
+**Architecture in one line:** issues live in a local Dolt DB; sync uses `refs/dolt/data` on your git remote; `.beads/issues.jsonl` is a passive export. See https://github.com/gastownhall/beads/blob/main/docs/SYNC_CONCEPTS.md for details and anti-patterns.
+
+## Agent Context Profiles
+
+The managed Beads block is task-tracking guidance, not permission to override repository, user, or orchestrator instructions.
+
+- **Conservative (default)**: Use `bd` for task tracking. Do not run git commits, git pushes, or Dolt remote sync unless explicitly asked. At handoff, report changed files, validation, and suggested next commands.
+- **Minimal**: Keep tool instruction files as pointers to `bd prime`; use the same conservative git policy unless active instructions say otherwise.
+- **Team-maintainer**: Only when the repository explicitly opts in, agents may close beads, run quality gates, commit, and push as part of session close. A current "do not commit" or "do not push" instruction still wins.
+
+## Session Completion
+
+This protocol applies when ending a Beads implementation workflow. It is subordinate to explicit user, repository, and orchestrator instructions.
+
+1. **File issues for remaining work** - Create beads for anything that needs follow-up
+2. **Run quality gates** (if code changed) - Tests, linters, builds
+3. **Update issue status** - Close finished work, update in-progress items
+4. **Handle git/sync by active profile**:
+   ```bash
+   # Conservative/minimal/default: report status and proposed commands; wait for approval.
+   git status
+
+   # Team-maintainer opt-in only, unless current instructions forbid it:
+   git pull --rebase
+   bd dolt push
+   git push
+   git status
+   ```
+5. **Hand off** - Summarize changes, validation, issue status, and any blocked sync/commit/push step
+
+**Critical rules:**
+- Explicit user or orchestrator instructions override this Beads block.
+- Do not commit or push without clear authority from the active profile or the current user request.
+- If a required sync or push is blocked, stop and report the exact command and error.
+<!-- END BEADS INTEGRATION -->
+
+<!-- BEGIN BEADS CODEX SETUP: generated by bd setup codex -->
+## Beads Issue Tracker
+
+Use Beads (`bd`) for durable task tracking in repositories that include it. Use the `beads` skill at `.agents/skills/beads/SKILL.md` (project install) or `~/.agents/skills/beads/SKILL.md` (global install) for Beads workflow guidance, then use the `bd` CLI for issue operations.
+
+### Quick Reference
+
+```bash
+bd ready                # Find available work
+bd show <id>            # View issue details
+bd update <id> --claim  # Claim work
+bd close <id>           # Complete work
+bd prime                # Refresh Beads context
+```
+
+### Rules
+
+- Use `bd` for all task tracking; do not create markdown TODO lists.
+- Run `bd prime` when Beads context is missing or stale. Codex 0.129.0+ can load Beads context automatically through native hooks; use `/hooks` to inspect or toggle them.
+- Keep persistent project memory in Beads via `bd remember`; do not create ad hoc memory files.
+
+**Architecture in one line:** issues live in a local Dolt DB; sync uses `refs/dolt/data` on your git remote; `.beads/issues.jsonl` is a passive export. See https://github.com/gastownhall/beads/blob/main/docs/SYNC_CONCEPTS.md for details and anti-patterns.
+<!-- END BEADS CODEX SETUP -->

CLAUDE.md

@@ -108,4 +108,59 @@ rm -f file                  # NOT: rm file
 2. **Run quality gates** - `cargo build --release && cargo test`
 3. **Close completed issues** - `bd close <id1> <id2> ...`
 4. **PUSH** - `git add -A && git commit -m "..." && git push`
-5. **Verify** - `git status` must show clean working tree
+5. **Verify** - `git status` must show clean working tree
+
+<!-- BEGIN BEADS INTEGRATION v:1 profile:minimal hash:6cd5cc61 -->
+## Beads Issue Tracker
+
+This project uses **bd (beads)** for issue tracking. Run `bd prime` to see full workflow context and commands.
+
+### Quick Reference
+
+```bash
+bd ready              # Find available work
+bd show <id>          # View issue details
+bd update <id> --claim  # Claim work
+bd close <id>         # Complete work
+```
+
+### Rules
+
+- Use `bd` for ALL task tracking — do NOT use TodoWrite, TaskCreate, or markdown TODO lists
+- Run `bd prime` for detailed command reference and session close protocol
+- Use `bd remember` for persistent knowledge — do NOT use MEMORY.md files
+
+**Architecture in one line:** issues live in a local Dolt DB; sync uses `refs/dolt/data` on your git remote; `.beads/issues.jsonl` is a passive export. See https://github.com/gastownhall/beads/blob/main/docs/SYNC_CONCEPTS.md for details and anti-patterns.
+
+## Agent Context Profiles
+
+The managed Beads block is task-tracking guidance, not permission to override repository, user, or orchestrator instructions.
+
+- **Conservative (default)**: Use `bd` for task tracking. Do not run git commits, git pushes, or Dolt remote sync unless explicitly asked. At handoff, report changed files, validation, and suggested next commands.
+- **Minimal**: Keep tool instruction files as pointers to `bd prime`; use the same conservative git policy unless active instructions say otherwise.
+- **Team-maintainer**: Only when the repository explicitly opts in, agents may close beads, run quality gates, commit, and push as part of session close. A current "do not commit" or "do not push" instruction still wins.
+
+## Session Completion
+
+This protocol applies when ending a Beads implementation workflow. It is subordinate to explicit user, repository, and orchestrator instructions.
+
+1. **File issues for remaining work** - Create beads for anything that needs follow-up
+2. **Run quality gates** (if code changed) - Tests, linters, builds
+3. **Update issue status** - Close finished work, update in-progress items
+4. **Handle git/sync by active profile**:
+   ```bash
+   # Conservative/minimal/default: report status and proposed commands; wait for approval.
+   git status
+
+   # Team-maintainer opt-in only, unless current instructions forbid it:
+   git pull --rebase
+   git push
+   git status
+   ```
+5. **Hand off** - Summarize changes, validation, issue status, and any blocked sync/commit/push step
+
+**Critical rules:**
+- Explicit user or orchestrator instructions override this Beads block.
+- Do not commit or push without clear authority from the active profile or the current user request.
+- If a required sync or push is blocked, stop and report the exact command and error.
+<!-- END BEADS INTEGRATION -->