When a step is expanded (e.g., implement -> implement.draft, implement.refine-1,
etc.), any steps that depended on the original step should now depend on the
last step of the expansion.
Call UpdateDependenciesForExpansion after both expand and map operations.
Fixes gt-8tmz.3
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When bd cook encounters a circular extends chain (A extends B extends A),
the error message now shows the full chain: "cycle-a -> cycle-b -> cycle-a"
instead of just "circular extends detected: cycle-a".
This makes debugging circular dependencies much easier by showing exactly
which formulas are involved in the cycle.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add DefaultMaxExpansionDepth constant and depth tracking in expandStep
to prevent runaway nested expansions. The limit applies to template
children during expansion.
Changes:
- Add DefaultMaxExpansionDepth = 5 constant
- Update expandStep to track depth and return error when exceeded
- Update ApplyExpansions callers to handle errors
- Add TestExpandStepDepthLimit test for depth limiting
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Distilled protos (via `bd mol distill`) now get bd-proto-xxx IDs.
Summary of distinct prefixes:
- bd-proto-xxx: templates created via distill
- bd-mol-xxx: instances created via pour
- bd-wisp-xxx: ephemeral instances via wisp create
- bd-xxx: regular issues
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add expand and map operators that apply macro-style template expansion:
- expand(target, template) - replace a single step with expanded template
- map(select, template) - replace all matching steps with expanded template
The expansion formula type (e.g., rule-of-five) uses a template field with
{target} and {target.description} placeholders that are substituted when
applied to target steps.
Changes:
- Add Template field to Formula struct for expansion formulas
- Add ExpandRule and MapRule types to ComposeRules
- Implement ApplyExpansions in new expand.go
- Add LoadByName method to Parser for loading expansion formulas
- Integrate expansion into bd cook command
- Add comprehensive tests
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Changed prefix logic to combine the database prefix with the type prefix:
- bd-wisp-xxx (was: wisp-xxx)
- bd-mol-xxx (was: mol-xxx)
This ensures IDs like hq-wisp-xxx at town level and gt-mol-xxx for gastown,
maintaining database namespace while adding type recognition.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Added type-specific ID prefixes for better visual recognition:
- `bd pour` now generates IDs with "mol-" prefix
- `bd wisp create` now generates IDs with "wisp-" prefix
- Regular issues continue using the configured prefix
Implementation:
- Added IDPrefix field to types.Issue (internal, not exported to JSONL)
- Added Prefix field to CloneOptions for spawning operations
- Added IDPrefix to RPC CreateArgs for daemon communication
- Updated storage layer to use issue.IDPrefix when generating IDs
- Updated pour.go and wisp.go to pass appropriate prefixes
This enables instant visual recognition of entity types and prevents
accidental modification of templates.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
- Change file extension from .formula.yaml to .formula.json
- Replace gopkg.in/yaml.v3 with encoding/json in parser
- Remove yaml struct tags, keep json tags only
- Update all test cases to use JSON format
- Update documentation references
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
bd should not assume specific orchestrator agents exist. Gates are just
data records - the orchestrator decides who processes them.
- Remove Assignee: deacon/ from gate creation
- Update help text to say orchestrator instead of Deacon patrol
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
bd mol run was a convenience combo (pour + assign + pin + start) that
felt like orchestration but lived in the data layer. This blurred the
architectural boundary between bd (data) and gt (orchestration).
- Delete cmd/bd/mol_run.go entirely
- Update mol.go help text to remove run reference
- Update mol_current.go to suggest bd pour instead
gt spawn will implement the orchestration combo by calling the atomic
bd commands (pour, update, pin) directly.
Closes bd-00u3
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Two issues fixed:
1. bd-c8d5: mol run only created partial children from proto
- Root cause: children with missing/wrong dependencies were not loaded
- Fix: loadDescendants now uses two strategies:
- Strategy 1: Check dependency records for parent-child relationships
- Strategy 2: Find hierarchical children by ID pattern (parent.N)
- This catches children that may have broken dependency data
2. bd-drcx: mol run now supports proto lookup by title
- Can use: bd mol run mol-polecat-work --var issue=gt-xxx
- Or by ID: bd mol run gt-lwuu --var issue=gt-xxx
- Title matching is case-insensitive and supports partial matches
- Shows helpful error on ambiguous matches
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace fetchAndRebaseInWorktree with contentMergeRecovery in pushFromWorktree.
The problem: When push fails due to non-fast-forward, the old code used git
rebase to recover. But git rebase is text-level and does not invoke the JSONL
merge driver. This could resurrect tombstones - if remote had a tombstone and
local had closed, the rebase would overwrite the tombstone.
The fix: Use the same content-level merge algorithm that PullFromSyncBranch
uses. This respects tombstone semantics - recent tombstones always win over
live issues.
Changes:
- Add contentMergeRecovery() that does content-level merge instead of rebase
- Update pushFromWorktree to call contentMergeRecovery
- Mark fetchAndRebaseInWorktree as deprecated (kept for reference)
- Add tests for tombstone preservation during merge recovery
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Wisps now use Wisp=true flag in the main database. The separate
.beads-wisp/ directory is no longer needed.
Removed:
- WispDirName constant
- FindWispDir()
- FindWispDatabasePath()
- NewWispStorage()
- EnsureWispGitignore()
- IsWispDatabase()
- All related tests
- .beads-wisp/ from .gitignore
The sync command's exportToJSONL function was not filtering wisps,
causing them to be re-added to JSONL during bd sync re-export step.
autoflush.go had wisp filtering but sync_export.go did not. Added
the same filtering logic to prevent wisps from being exported to JSONL.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Remove cross-store squash logic from mol_squash.go
- Delete runWispSquash() and squashWispToPermanent() functions
- Simplify runMolSquash() to work with main store only
- Update mol_burn.go to work with main database
- Remove .beads-wisp/ directory references
- Look for Wisp=true issues in main store instead
- Update mol_bond.go to use Wisp flag instead of separate store
- --wisp now creates issues with Wisp=true in main store
- --pour creates issues with Wisp=false (persistent)
- Update bondProtoMol signature to accept both flags
- Deprecate wisp storage functions in beads.go
- WispDirName, FindWispDir, FindWispDatabasePath
- NewWispStorage, EnsureWispGitignore, IsWispDatabase
- All marked deprecated with reference to bd-bkul
- Remove obsolete cross-store squash tests
- TestSquashWispToPermanent
- TestSquashWispToPermanentWithSummary
- TestSquashWispToPermanentKeepChildren
All tests pass. Build succeeds.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Progress on eliminating separate .beads-wisp/ directory:
- Add --wisp flag to bd create (creates issue with Wisp=true)
- Update bd wisp create to use main db instead of separate wisp storage
- Update bd wisp list to query main db with Wisp filter
- Update bd wisp gc to work with main database
- Add Wisp field to RPC ListArgs for daemon mode support
- Fix terminology: use "old/abandoned" for time-based cleanup,
reserve "stale" for graph-pressure staleness (per Gas Town taxonomy)
Still TODO:
- Finish mol squash simplification (remove cross-store logic)
- Remove runWispSquash and squashWispToPermanent functions
- Update mol burn similarly
- Deprecate .beads-wisp/ functions in internal/beads/beads.go
- Test all changes
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Completely rewrote the molecular chemistry doc to be more practical:
- Start with execution semantics (what users care about)
- TL;DR section at top with 5 key concepts
- Explain dependency types and blocking behavior
- Clarify molecules = epics (no special types needed)
- Move chemistry metaphor to secondary section
- Add common patterns (sequential, fanout, dynamic bonding)
- Keep agent pitfalls and quick reference
The doc now reads like a reference manual with examples rather than
a philosophical treatise on work composition.
Filed gt-qe9w for Gas Town docs to follow same pattern.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds release notes for v0.36.0 including:
- Formula system and gate issue type
- bd list --pretty --watch enhancements
- Child→parent dep prevention (LLM temporal trap)
- Multiple bug fixes
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Highlights that this prevents a common LLM temporal reasoning trap
where 'Phase 1 before Phase 2' gets modeled as Phase 1 blocking Phase 2
instead of Phase 2 depending on Phase 1.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
