This is the final phase of the Edge Schema Consolidation. It removes
the deprecated edge fields (RepliesTo, RelatesTo, DuplicateOf, SupersededBy)
from the Issue struct and all related code.
Changes:
- Remove edge fields from types.Issue struct
- Remove edge field scanning from queries.go and transaction.go
- Update graph_links_test.go to use dependency API exclusively
- Update relate.go to use AddDependency/RemoveDependency
- Update show.go with helper functions for thread traversal via deps
- Update mail_test.go to verify thread links via dependencies
- Add migration 022 to drop columns from issues table
- Fix cycle detection to allow bidirectional relates-to links
- Fix migration 022 to disable foreign keys before table recreation
All edge relationships now use the dependencies table exclusively.
The old Issue fields are fully removed.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Commands relate, unrelate, duplicate, and supersede now properly
use RPC Update when daemonClient is available, instead of always
calling store.UpdateIssue() directly and bypassing the daemon.
Added RelatesTo, DuplicateOf, and SupersededBy fields to UpdateArgs
in the RPC protocol, and updated server_issues_epics.go to handle them.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add migration to convert existing issue fields to dependency edges:
- replies_to -> replies-to dependency with thread_id
- relates_to -> relates-to dependencies (JSON array)
- duplicate_of -> duplicates dependency
- superseded_by -> supersedes dependency
The migration is idempotent (INSERT OR IGNORE) so it does not duplicate
edges that were already created by Phase 2 dual-write.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When issue fields (replies_to, relates_to, duplicate_of, superseded_by)
are set during CreateIssue or UpdateIssue, we now ALSO create the
corresponding dependency edges. This enables gradual migration to
edge-based storage while maintaining backward compatibility.
Changes:
- createGraphEdgesFromIssueFields: handles CreateIssue dual-write
- createGraphEdgesFromUpdates: handles UpdateIssue dual-write
- Replies-to edges include thread_id for efficient thread queries
- Uses INSERT OR IGNORE to handle idempotency
The dual-write ensures both field and dependency stay in sync during
the migration period.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add metadata and thread_id columns to dependencies table to support:
- Edge metadata: JSON blob for type-specific data (similarity scores, etc.)
- Thread queries: O(1) conversation threading via thread_id
Changes:
- New migration 020_edge_consolidation.go
- Updated Dependency struct with Metadata and ThreadID fields
- Added new entity types: authored-by, assigned-to, approved-by
- Relaxed DependencyType validation (any non-empty string ≤50 chars)
- Added IsWellKnown() and AffectsReadyWork() methods
- Updated SQL queries to include new columns
- Updated tests for new behavior
This enables HOP knowledge graph requirements and Reddit-style threading.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The countDBIssuesFast() fallback path used SearchIssues without
IncludeTombstones, returning only live issues (161). Meanwhile
countIssuesInJSONL counts all lines including tombstones (221).
This mismatch caused false "stale DB detected" warnings on every
sync, even when DB and JSONL were in sync.
Fix: Set IncludeTombstones: true in the fallback SearchIssues call.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Removes the legacy YAML-based simple template system that provided
bug/epic/feature templates for --from-template flag on bd create.
Removed:
- cmd/bd/templates/bug.yaml, epic.yaml, feature.yaml
- Template struct and all YAML loading functions in template.go
- --from-template flag from bd create command
- template_security_test.go (tested removed functions)
- YAML template tests from template_test.go
The Beads template system remains (epics with "template" label,
instantiated via bd template instantiate with variable substitution).
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add --assignee flag to `bd template instantiate` for work delegation
- Assigns the root epic to specified agent/user
- Child issues retain their template-defined assignees
- Enables Gas Town orchestration: instantiate + assign in one step
- Add missing --identity flag to `bd mail inbox` for consistency
- All mail subcommands now support --identity override
- Delete obsolete HANDOFF-template-redesign.md (work complete)
- Add test for assignee override behavior
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
No point warning about orphaned issues that are already closed or
tombstoned - they're dead either way.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Orphan detection was reporting tombstoned issues (already deleted) as
orphans, causing repeated warnings during sync. Filter out status='tombstone'
from the orphan query.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
Implements native Beads templates as an alternative to YAML templates:
- Templates are epics with the "template" label and {{variable}} placeholders
- `bd template list` shows both YAML and Beads templates
- `bd template show <id>` displays template structure and variables
- `bd template instantiate <id> --var key=value` clones subgraph with substitution
Key implementation:
- loadTemplateSubgraph: Recursively loads epic and all descendants
- cloneSubgraph: Creates new issues with ID remapping in a transaction
- extractVariables/substituteVariables: {{name}} pattern handling
Closes bd-r6a.2, bd-r6a.4
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove the entire YAML-based workflow system in preparation for
redesigning templates as native Beads.
Removed:
- cmd/bd/templates/workflows/*.yaml
- cmd/bd/workflow.go
- internal/types/workflow.go (WorkflowTemplate types)
The new design will use regular Beads with a template label,
and a clone-with-substitution operation for instantiation.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Allows bypassing preflight checks when needed (e.g., testing).
Use with caution - preflight checks exist for safety.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds `bd workflow` command group that creates epics with dependent child tasks
from YAML templates. This enables structured multi-step workflows like version
bumps where agents can work through tasks with verification and dependencies.
Commands:
- `bd workflow list` - List available workflow templates
- `bd workflow show <name>` - Show template details and task graph
- `bd workflow create <name> --var key=value` - Instantiate workflow
- `bd workflow status <epic-id>` - Show workflow progress
- `bd workflow verify <task-id>` - Run verification command
Features:
- Variable substitution with {{var}} syntax
- Built-in variables: {{today}}, {{user}}
- Preflight checks before workflow creation
- Hierarchical task IDs under epic (bd-xxx.1, bd-xxx.2)
- Dependency graph between tasks
- Verification commands embedded in task descriptions
Includes built-in `version-bump` template with 21 tasks covering:
- All 10+ version files
- check-versions.sh verification
- Git commit, tag, push
- CI monitoring (goreleaser, npm, pypi, homebrew)
- Local machine upgrades
- Final verification
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Files missed in manual version bump:
- .claude-plugin/plugin.json
- .claude-plugin/marketplace.json
- integrations/beads-mcp/pyproject.toml
- integrations/beads-mcp/__init__.py
- Hook templates
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
npm deprecated classic tokens and now requires either granular tokens
with 2FA or OIDC trusted publishing. This updates the workflow to use
the latter, which is npm recommended approach for CI/CD.
Requires configuring trusted publisher on npmjs.com:
- Organization: steveyegge
- Repository: beads
- Workflow: release.yml
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove ClearDirtyIssues() which had a race condition that could lose
dirty issues if export failed partway through. All callers now use
ClearDirtyIssuesByID() which only clears specific exported issues.
- Remove from Storage interface
- Remove from SQLite and Memory implementations
- Update 6 test call sites to use ClearDirtyIssuesByID()
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds "Dependencies: Think Needs, Not Before" section with the
WRONG/RIGHT example pair to help agents avoid the temporal
language trap that inverts dependency direction.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds a "Writing Self-Contained Issues" section to the onboarding output
that instructs AI agents to create fully context-independent issues.
Includes required elements (summary, files, steps, examples) and shows
good vs bad examples.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- bd-06px: Add --no-git-history flag to import command for sync subprocess compatibility
- bd-0zp7: Add missing hook calls (EventMessage in mail reply, EventClose in mail ack)
- bd-hy9p: Implement --body-file and --description-file flags for reading descriptions from files
Also closed stale issues that were already fixed:
- bd-0d5p: macOS test timeout (already fixed with SysProcAttr)
- bd-7yg: Merge driver placeholders (already using correct %A %O %A %B)
- bd-4ri: Test deadlock (test passes in 0.04s now)
- bd-b3og: TestImportBugIntegration (test no longer exists)
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Root cause: Previous fix only cleaned beads-sync branch, not main.
During 3-way merge, orphans were re-introduced from main.
This export is from clean DB (0 orphaned issues).
Also force-resetting beads-sync to match.
Adds back third-party tools removed in succinct README PR.
Includes beads.el Emacs package (closes#610).
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Three changes to fix deleted issues resurrecting during bd sync:
1. daemon handleDelete now uses CreateTombstone instead of DeleteIssue
- internal/rpc/server_issues_epics.go
2. sync.go exportToJSONL now includes IncludeTombstones:true
- cmd/bd/sync.go
3. server_export_import_auto.go handleExport and auto-export now include
tombstones in SearchIssues filter
- internal/rpc/server_export_import_auto.go
Also adds README.md documentation for sync.branch mode (bd-dsdh):
- Explains "always dirty" working tree behavior
- Shell alias tip: gs='git status -- ":!.beads/"'
- When to use bd sync --merge
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The sync.branch workflow copies JSONL to main working dir without
committing, which blocked bd sync --merge (required clean working dir).
Changes:
- Exclude .beads/ from dirty check in mergeSyncBranch
- Restore .beads/ to HEAD before merge to prevent conflicts
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Move runHook into build-tagged implementations (unix/windows) to keep unix syscalls off Windows builds.
- In unix implementation, guard nil Process, return wrapped kill errors except ESRCH, and document linkage to TestRunSync_KillsDescendants.
- On Windows, best-effort kill on timeout retains prior behavior.
- In tests, move testing.Short earlier and keep descendant-kill coverage on Linux.
Root cause: The merge driver matched issues by IssueKey (ID+CreatedAt+CreatedBy).
When timestamp precision differed (e.g., with/without nanoseconds), the same
issue was treated as two different issues, causing both tombstone and closed
versions to appear in the merge result.
Fix: Added ID-based fallback matching in merge3WayWithTTL. When key-based
matching fails but the same ID exists in the other side, use that for merging.
Also track processed IDs to prevent duplicates.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
