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11 Commits

Author SHA1 Message Date
Steve Yegge
e068ac574f refactor: Simplify wisp architecture - badges not separate storage 
Wisps are now just issues with Wisp=true flag in the main database,
not exported to JSONL. Removes all references to .beads-wisp/ directory.

- Update docs: CLAUDE.md, CLI_REFERENCE.md, MOLECULES.md, DELETIONS.md
- Update code comments: wisp.go
- Update changelog and info.go version notes

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2025-12-25 01:49:57 -08:00
Steve Yegge
5e971bd90a docs: add molecular chemistry documentation (bd-ul59) 
Create docs/MOLECULES.md with comprehensive coverage of:
- Layer cake architecture (formulas → protos → molecules → epics → issues)
- Phase metaphor (solid/proto, liquid/mol, vapor/wisp)
- Phase transitions (pour, wisp create, squash, burn)
- Bonding patterns (proto+proto, proto+mol, mol+mol)
- Agent pitfalls (temporal language, forgetting to squash)
- Orphan vs stale matrix
- Progress tracking (computed, not stored)
- Parallelism model (default parallel, opt-in sequential)

Update CLI_REFERENCE.md with Molecular Chemistry section covering:
- Proto/template commands
- Pour command
- Wisp commands
- Bonding commands
- Squash and burn commands

Update ARCHITECTURE.md with cross-reference to new MOLECULES.md.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2025-12-24 19:31:14 -08:00
Andrei Onel
9382aa34fa Update CLI reference with new --body-file options (#627) 
Documentation update for --body-file option
 2025-12-18 18:25:09 -08:00
Steve Yegge
83ae110508 refactor: Remove legacy MCP Agent Mail integration (bd-6gd) 
Remove the external MCP Agent Mail server integration that required
running a separate HTTP server and configuring environment variables.

The native `bd mail` system (stored as git-synced issues) remains
unchanged and is the recommended approach for inter-agent messaging.

Files removed:
- cmd/bd/message.go - Legacy `bd message` command
- integrations/beads-mcp/src/beads_mcp/mail.py, mail_tools.py
- lib/beads_mail_adapter.py - Python adapter library
- examples/go-agent/ - Agent Mail-focused example
- examples/python-agent/agent_with_mail.py, AGENT_MAIL_EXAMPLE.md
- docs/AGENT_MAIL*.md, docs/adr/002-agent-mail-integration.md
- tests/integration/test_agent_race.py, test_mail_failures.py, etc.
- tests/benchmarks/ - Agent Mail benchmarks

Updated documentation to remove Agent Mail references while keeping
native `bd mail` documentation intact.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2025-12-17 23:14:23 -08:00
Jordan Hubbard
e0528de590 feat: add Factory.ai (Droid) support to bd setup command (#598) 
Adds Factory.ai (Droid) support to bd setup command via AGENTS.md integration.

- New command: bd setup factory (with --check and --remove flags)
- Creates/updates AGENTS.md with beads workflow instructions
- Uses HTML comment markers for safe idempotent updates
- Comprehensive documentation

Thanks @jordanhubbard!
 2025-12-16 13:42:43 -08:00
Steve Yegge
dedfc43d1f Merge GH#409 2025-12-16 01:19:07 -08:00
Steve Yegge
166d66205c docs: update beads.jsonl references to issues.jsonl 
Fixes GH#409 - Documentation inconsistently referred to beads.jsonl
as the canonical filename when issues.jsonl has been the default
since v0.25.1 (bd-6xd).

Updated files:
- docs/ARCHITECTURE.md
- docs/CLI_REFERENCE.md
- docs/PROTECTED_BRANCHES.md
- docs/ADVANCED.md
- docs/GIT_INTEGRATION.md
- docs/MULTI_REPO_AGENTS.md
- docs/MULTI_REPO_MIGRATION.md
- docs/TROUBLESHOOTING.md
- examples/*/README.md
- skills/beads/references/CLI_REFERENCE.md

Note: beads.jsonl is still supported for backward compatibility.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2025-12-16 01:08:46 -08:00
Steve Yegge
39a58fd085 docs: document bd setup command 
Add comprehensive documentation for the bd setup command which was
largely undocumented (GH#518):

- CLI_REFERENCE.md: Add new "Editor Integration" section documenting
  bd setup claude/cursor/aider commands with all flags
- INSTALLING.md: Fix incorrect reference to "bd hooks install" for
  editor integration - should be "bd setup <editor>"
- CLAUDE_INTEGRATION.md: Add Installation section with bd setup claude
  examples

Fixes: GH#518

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
 2025-12-16 01:08:42 -08:00
Steve Yegge
e0e6dff87f docs: Complete import.orphan_handling documentation (bd-9cdc) 
Added comprehensive documentation for import orphan handling configuration
across all relevant documentation files:

- AGENTS.md: Added "Import Configuration" section with detailed mode
  explanations and usage guidance
- README.md: Documented orphan handling in Export/Import section with
  examples of all four modes
- TROUBLESHOOTING.md: Added "Import fails with missing parent errors"
  troubleshooting section with resurrection examples and prevention tips
- CLI_REFERENCE.md: Expanded Import/Export section with --orphan-handling
  flag documentation and cross-references

Documented resurrection behavior:
- Tombstone creation (Status=Closed, Priority=4)
- JSONL history search for deleted parents
- Best-effort dependency resurrection
- Hierarchical ancestor chain handling

Closes bd-9cdc

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Co-Authored-By: Claude <noreply@anthropic.com>
 2025-11-24 01:08:08 -08:00
Steve Yegge
58fe00057c feat: Complete GH #353 follow-up phases (bd-9nw, bd-u3t, bd-e0o) 
Implements all three follow-up phases for sandbox environment support:

**Phase 1 (bd-9nw): Documentation** ✅
- Comprehensive sandbox troubleshooting section in TROUBLESHOOTING.md
  - Detailed symptoms, root causes, and escape hatches
  - Step-by-step troubleshooting workflow
  - Comparison table for --sandbox, --force, and --allow-stale flags
- Global flags section added to CLI_REFERENCE.md
  - Documents --sandbox, --allow-stale, and --force flags
  - Usage examples and when to use each flag
- GitHub issue #353 comment with immediate workarounds

**Phase 2 (bd-u3t): Sandbox Auto-Detection** ✅
- Automatic sandbox detection using syscall.Kill permission checks
  - cmd/bd/sandbox_unix.go: Unix/Linux/macOS implementation
  - cmd/bd/sandbox_windows.go: Windows stub (conservative approach)
  - cmd/bd/sandbox_test.go: Comprehensive test coverage
- Auto-enables sandbox mode when detected
  - Shows: "ℹ️  Sandbox detected, using direct mode"
  - Respects explicit --sandbox or --no-daemon flags
- Updated documentation to reflect auto-detection (v0.21.1+)

**Phase 3 (bd-e0o): Enhanced Daemon Robustness** ✅
- Permission-aware process checks in cmd/bd/daemon_unix.go
  - Correctly handles EPERM (operation not permitted) from syscall.Kill
  - Treats EPERM as "process exists but not signable" = running
  - Prevents false negatives in sandboxed environments
- Metadata health check in cmd/bd/daemon_event_loop.go
  - Periodic verification that metadata is accessible
  - Helps detect external import operations (bd import --force)
  - Non-fatal logging for diagnostics
- Comprehensive test suite in cmd/bd/daemon_unix_test.go
  - Self-check, init process, nonexistent process, parent process tests

**Impact:**
- Codex users: No manual intervention needed, auto-detected
- Stuck states: Three escape hatches (--sandbox, --force, --allow-stale)
- Daemon robustness: Handles permission-restricted environments gracefully
- All three follow-up issues (bd-9nw, bd-u3t, bd-e0o) closed

**Files changed:**
- cmd/bd/main.go: Auto-detection logic in PersistentPreRun
- cmd/bd/sandbox_unix.go: Unix sandbox detection (new)
- cmd/bd/sandbox_windows.go: Windows sandbox detection stub (new)
- cmd/bd/sandbox_test.go: Sandbox detection tests (new)
- cmd/bd/daemon_unix.go: Permission-aware isProcessRunning()
- cmd/bd/daemon_unix_test.go: Process check tests (new)
- cmd/bd/daemon_event_loop.go: Metadata health check
- docs/TROUBLESHOOTING.md: Comprehensive sandbox section
- docs/CLI_REFERENCE.md: Global flags documentation

Closes bd-9nw, bd-u3t, bd-e0o
Related: GH #353

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Co-Authored-By: Claude <noreply@anthropic.com>
 2025-11-21 19:32:45 -05:00
Steve Yegge
826a3b2047 Refactor AGENTS.md: extract supplemental docs 
- Create docs/DAEMON.md (daemon mgmt, event-driven mode)
- Create docs/GIT_INTEGRATION.md (worktrees, conflicts, merge drivers)
- Create docs/CLI_REFERENCE.md (comprehensive command examples)
- Reduce AGENTS.md from 1047 → 906 lines (13% reduction)
- Add Agent Mail optional workflow section (bd-2cvu)

Improves navigability while preserving all content.

Amp-Thread-ID: https://ampcode.com/threads/T-f8161cc4-d6d2-4f23-8854-4834dbdedb26
Co-authored-by: Amp <amp@ampcode.com>
 2025-11-08 01:03:28 -08:00