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docs: Add comprehensive Agent Mail integration guide

Browse Source 
- Installation and quick start
- Architecture and coordination flow
- Configuration reference (environment variables)
- When to use vs skip Agent Mail
- Multi-machine deployment patterns
- Troubleshooting and FAQ
- Migration guide from git-only mode

Closes bd-xzrv

Amp-Thread-ID: https://ampcode.com/threads/T-e8cf1b4b-38ae-4f6b-ae17-8b960d31608e
Co-authored-by: Amp <amp@ampcode.com>
This commit is contained in:
Steve Yegge
2025-11-08 00:49:41 -08:00
parent bd59973170
commit 9cffd39246
2 changed files with 528 additions and 1 deletions
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.beads/beads.jsonl
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@@ -347,7 +347,7 @@
{"id":"bd-ww0g","content_hash":"973e5e6eb58975fcbe80f804b69a900cde824af4b51243737ef5fca404d0b1c1","title":"MCP server: \"No workspace set\" and \"chunk longer than limit\" errors","description":"Two related errors reported in beads-mcp v0.21:\n\n**Error 1: \"No workspace set\" after successful set_context**\n```\n✓ Set beads context\n✗ list\n Error calling tool 'list': No workspace set. Either provide workspace_root\n parameter or call set_context() first.\n```\n\nHypothesis: Environment variable persistence issue between MCP tool calls, or ContextVar not being set correctly by @with_workspace decorator.\n\n**Error 2: \"Separator is found, but chunk is longer than limit\"**\n```\n✗ list\n Error calling tool 'list': Separator is found, but chunk is longer than limit\n```\n\nHypothesis: MCP protocol output size limit exceeded. Large issue databases may produce JSON output that exceeds MCP stdio buffer limits.\n\nPlatform: Fedora 43, using copilot-cli with Sonnet 4.5\n\nWorkaround: CLI works fine (`bd list --status open --json`)","notes":"## Fixes Implemented\n\n**Issue 1: \"No workspace set\" after successful set_context** ✅ FIXED\n\nRoot cause: os.environ doesn't persist across MCP tool calls. When set_context() set BEADS_WORKING_DIR in os.environ, that change was lost on the next tool call.\n\nSolution:\n- Added module-level _workspace_context dict for persistent storage (server.py:51)\n- Modified set_context() to store in both persistent dict and os.environ (server.py:265-287)\n- Modified with_workspace() decorator to check persistent context first (server.py:129-133)\n- Updated where_am_i() to check persistent context (server.py:302-330)\n\n**Issue 2: \"chunk longer than limit\"** ✅ FIXED\n\nRoot cause: MCP stdio protocol has buffer limits. Large issue lists with full dependencies/dependents exceed this.\n\nSolution:\n- Reduced default list limit from 50 to 20 (server.py:356, models.py:122)\n- Reduced max list limit from 1000 to 100 (models.py:122)\n- Strip dependencies/dependents from list() and ready() responses (server.py:343-350, 368-373)\n- Full dependency details still available via show() command\n\n## Testing\n\n✅ Python syntax validated with py_compile\n✅ Changes are backward compatible\n✅ Persistent context falls back to os.environ for compatibility\n\nUsers should now be able to call set_context() once and have it persist across all subsequent tool calls. Large databases will no longer cause buffer overflow errors.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-07T14:32:18.315155-08:00","updated_at":"2025-11-07T21:02:55.470937-08:00","closed_at":"2025-11-07T16:53:46.929942-08:00","source_repo":"."}
{"id":"bd-x47","content_hash":"0b5f05ca037293f7be36f9a080da731e67bec96ba68e2b7cbeb589cc60343225","title":"Add guidance for self-hosting projects","description":"The contributor-workflow-analysis.md is optimized for OSS contributors making PRs to upstream projects. However, it doesn't address projects like VC that use beads for their own development (self-hosting).\n\nSelf-hosting projects differ from OSS contributors:\n- No upstream/downstream distinction (they ARE the project)\n- May run automated executors (not just humans)\n- In bootstrap/early phase (stability matters)\n- Single team/owner (not multiple contributors with permissions)\n\nGuidance needed on:\n- When self-hosting projects should stay single-repo (default, recommended)\n- When they should adopt multi-repo (team planning, multi-phase dev)\n- How automated executors should handle multi-repo (if at all)\n- Special considerations for projects in bootstrap phase\n\nExamples of self-hosting projects: VC (building itself with beads), internal tools, pet projects","acceptance_criteria":"- Section added: 'For Projects Using Beads for Self-Hosting'\n- Clear guidance on when to stay single-repo vs adopt multi-repo\n- Recommendations for automated executor behavior with multi-repo\n- Bootstrap phase considerations documented","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-03T20:24:27.805341-08:00","updated_at":"2025-11-05T14:16:34.69662-08:00","closed_at":"2025-11-05T14:16:34.69662-08:00","source_repo":"."}
{"id":"bd-xo6b","content_hash":"a8f6100ae8d6569c75565d5a1aacbc0e55806fab917399ab473fb212fa694b80","title":"Review multi-repo deletion tracking implementation","description":"Thoroughly review the multi-repo deletion tracking fix (bd-4oob):\n\nFiles changed:\n- cmd/bd/deletion_tracking.go: Added getMultiRepoJSONLPaths() helper\n- cmd/bd/daemon_sync.go: Updated snapshot capture/update logic for multi-repo\n- cmd/bd/deletion_tracking_test.go: Added 2 new tests (287 lines)\n\nReview focus areas:\n1. Correctness: Does getMultiRepoJSONLPaths() handle all edge cases?\n2. Performance: Calling getMultiRepoJSONLPaths() 3x per sync (snapshot capture, merge, base update) - should we cache?\n3. Error handling: What if some repos fail snapshot operations but others succeed?\n4. Race conditions: Multiple daemons in different repos?\n5. Test coverage: Are TestMultiRepoDeletionTracking and TestMultiRepoSnapshotIsolation sufficient?\n6. Path handling: Absolute vs relative paths, tilde expansion\n\nThis is fresh code - needs careful review before considering deletion tracking production-ready.","notes":"Code review completed. Overall assessment: Core deletion tracking logic is sound, but error handling and path handling issues make this not yet production-ready for multi-repo scenarios.\n\nKey findings:\n\nCRITICAL ISSUES (Priority 1):\n1. Inconsistent error handling in daemon_sync.go - snapshot/merge fail hard but base update warns. Can leave DB in inconsistent state with no rollback. See bd-sjmr.\n2. No path normalization in getMultiRepoJSONLPaths() - tilde expansion, relative paths, duplicates not handled. See bd-iye7.\n\nSHOULD FIX (Priority 2):\n3. Missing test coverage for edge cases - empty paths, duplicates, partial failures. See bd-kdoh.\n4. Performance - getMultiRepoJSONLPaths() called 3x per sync (minor issue). See bd-we4p.\n\nWHAT WORKS WELL:\n- Atomic file operations with PID-based temp files\n- Good snapshot isolation between repos\n- Race condition protection via exclusive locks\n- Solid test coverage for happy path scenarios\n\nVERDICT: Address bd-iye7 and bd-sjmr before considering deletion tracking production-ready for multi-repo mode.\n\nDetailed review notes available in conversation history.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-06T19:23:52.402949-08:00","updated_at":"2025-11-06T19:32:34.160341-08:00","closed_at":"2025-11-06T19:32:34.160341-08:00","source_repo":".","dependencies":[{"issue_id":"bd-xo6b","depends_on_id":"bd-rbxi","type":"parent-child","created_at":"2025-11-06T19:23:52.403723-08:00","created_by":"daemon"}]}
{"id":"bd-xzrv","content_hash":"d5833f7953e5c353b9b5466c054d5bb8472bf8139570326353ec6402f368f8f4","title":"Write Agent Mail integration guide","description":"Comprehensive guide for setting up and using Agent Mail with Beads.\n\nAcceptance Criteria:\n- Installation instructions\n- Configuration (environment variables)\n- Architecture diagram\n- Benefits and tradeoffs\n- When to use vs not use\n- Troubleshooting section\n- Migration from git-only mode\n\nFile: docs/AGENT_MAIL.md\n\nSections:\n- Quick start\n- How it works\n- Integration points\n- Graceful degradation\n- Multi-machine deployment\n- FAQ","status":"open","priority":1,"issue_type":"task","created_at":"2025-11-07T22:42:51.231066-08:00","updated_at":"2025-11-07T22:42:51.231066-08:00","source_repo":".","dependencies":[{"issue_id":"bd-xzrv","depends_on_id":"bd-fzbg","type":"blocks","created_at":"2025-11-07T22:42:51.232246-08:00","created_by":"daemon"}]}
{"id":"bd-xzrv","content_hash":"bc0097eb1382f92d5f2a80189a9a7da19a4cc2a11ac3beda5af4c93a55692227","title":"Write Agent Mail integration guide","description":"Comprehensive guide for setting up and using Agent Mail with Beads.\n\nAcceptance Criteria:\n- Installation instructions\n- Configuration (environment variables)\n- Architecture diagram\n- Benefits and tradeoffs\n- When to use vs not use\n- Troubleshooting section\n- Migration from git-only mode\n\nFile: docs/AGENT_MAIL.md\n\nSections:\n- Quick start\n- How it works\n- Integration points\n- Graceful degradation\n- Multi-machine deployment\n- FAQ","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-07T22:42:51.231066-08:00","updated_at":"2025-11-08T00:40:38.798162-08:00","closed_at":"2025-11-08T00:40:38.798162-08:00","source_repo":".","dependencies":[{"issue_id":"bd-xzrv","depends_on_id":"bd-fzbg","type":"blocks","created_at":"2025-11-07T22:42:51.232246-08:00","created_by":"daemon"}]}
{"id":"bd-yek6","content_hash":"f155913af8c58c0a7ea3da6a7d9e232e8cb29c3825f2d6f272a5417a449692a9","title":"CLI tests (cli_fast_test.go) are slow and should be integration tests","description":"The TestCLI_* tests in cmd/bd/cli_fast_test.go are taking 4-5 seconds each (40+ seconds total), making them the slowest part of the fast test suite.\n\nCurrent timings:\n- TestCLI_Import: 4.73s\n- TestCLI_Blocked: 4.33s \n- TestCLI_DepTree: 4.15s\n- TestCLI_Close: 3.59s\n- TestCLI_DepAdd: 3.50s\n- etc.\n\nThese tests compile the bd binary once in init(), but then execute it multiple times per test with filesystem operations. Despite being named \"fast\", they're actually end-to-end CLI integration tests.\n\nOptions:\n1. Tag with //go:build integration (move to integration suite)\n2. Optimize: Use in-memory databases, reduce exec calls, better parallelization\n3. Keep as-is but understand they're the baseline for \"fast\" tests\n\nTotal test suite currently: 13.8s (cmd/bd alone is 12.8s, and most of that is these CLI tests)","notes":"Fixed by reusing existing bd binary from repo root instead of rebuilding.\n\nBefore: 15+ minutes (rebuilding binary for every test package)\nAfter: ~12 seconds (reuses pre-built binary)\n\nThe init() function now checks for ../../bd first before falling back to building. This means `go build \u0026\u0026 go test` is now fast.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-05T20:19:12.822543-08:00","updated_at":"2025-11-05T20:31:19.321787-08:00","closed_at":"2025-11-05T20:31:19.321787-08:00","source_repo":"."}
{"id":"bd-z3s3","content_hash":"24d99dc1a9a5f35af962137f5709d4b0f1b6a9ec91511c30a2517d790640cce8","title":"Create deployment scripts for GCP","description":"Automated provisioning scripts for GCP Compute Engine deployment.\n\nAcceptance Criteria:\n- Terraform/gcloud scripts\n- Static IP allocation\n- Firewall rules\n- NGINX reverse proxy config\n- TLS setup (Let's Encrypt)\n- Systemd service file\n\nFile: deployment/agent-mail/gcp/","status":"open","priority":3,"issue_type":"task","created_at":"2025-11-07T22:43:43.294839-08:00","updated_at":"2025-11-07T22:43:43.294839-08:00","source_repo":".","dependencies":[{"issue_id":"bd-z3s3","depends_on_id":"bd-9li4","type":"blocks","created_at":"2025-11-07T23:04:27.982336-08:00","created_by":"daemon"}]}
{"id":"bd-z528","content_hash":"3f332e9997d2b7eb0af23885820df5f607fe08671a2615cadec941bbe7d36f68","title":"Prevent test pollution in production database","description":"The bd-vxdr cleanup revealed test issues were created during manual testing in the production workspace (Nov 2-4, template feature development).\n\n**Root cause:** Manual testing with `./bd create \"Test issue\"` pollutes the production .beads database.\n\n**Prevention strategies:**\n1. Use TEST_DB environment variable for manual testing\n2. Add warning when creating issues with \"Test\" prefix\n3. Improve developer docs about testing workflow\n4. Consider adding `bd test-mode` command for isolated testing","notes":"**Implementation completed:**\n\n1. ✅ Added warning when creating issues with \"Test\" prefix in production database\n - Shows yellow warning with ⚠ symbol\n - Suggests using BEADS_DB for isolated testing\n - Warning appears in create.go after title validation\n\n2. ✅ Documented BEADS_DB testing workflow in AGENTS.md\n - Added \"Testing Workflow\" section in Development Guidelines\n - Includes manual testing examples with BEADS_DB\n - Includes automated testing examples with t.TempDir()\n - Clear warning about not polluting production database\n\n3. ⚠️ Decided against bd test-mode command\n - BEADS_DB already provides simple, flexible isolation\n - Additional command would add complexity without much benefit\n - Current approach follows Unix philosophy (env vars for config)\n\n**Files modified:**\n- cmd/bd/create.go - Added Test prefix warning\n- AGENTS.md - Added Testing Workflow section\n\n**Testing:**\n- Verified warning appears when creating \"Test\" prefix issues\n- Verified BEADS_DB isolation works correctly\n- Built successfully with `go build`","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-07T16:07:28.255289-08:00","updated_at":"2025-11-07T23:18:08.386514-08:00","closed_at":"2025-11-07T22:43:28.669908-08:00","source_repo":"."}