- Move write stream creation after redirect handling to avoid orphan
streams that keep file handles open
- Add 100ms delay after file.close() on Windows to ensure handle release
- Fixes "The process cannot access the file" error during extraction
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update help text to clarify mol/wisp/epic support (not just epics)
- Add daemon support (no longer requires --no-daemon)
- Add -o shorthand for --output flag
- Update use cases to match new architecture
Part of bd-1dez.1
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Fix YAML → JSON references in formula.go and types.go
- Update MOLECULES.md with ephemeral proto architecture
- Add Distillation section: extract formulas from completed work
- Add Sharing section: Mol Mall formula marketplace
- Update Layer Cake diagram to show ephemeral proto flow
Related: bd-1dez (Mol Mall epic)
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add --mode flag (compile/runtime) and --var flag to bd cook command.
Compile-time mode (default):
- Keeps {{variable}} placeholders intact
- Use for: modeling, estimation, contractor handoff
Runtime mode (triggered by --var or --mode=runtime):
- Substitutes variables with provided values
- Validates all required variables have values
- Use for: final validation before pour
Also updates --dry-run output to clearly show which mode is active
and display substituted values in runtime mode.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Test cases for:
- Unary minus in expression: 3*-2 -> -6
- Parenthesized negative: (-5) -> -5
- Unary minus after power: 2^-1 -> 0 (truncated)
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add support for for-each expansion over computed ranges:
loop:
range: "1..2^{disks}-1" # Evaluated at cook time
var: move_num
body: [...]
Features:
- Range field in LoopSpec for computed iterations
- Var field to expose iteration value to body steps
- Expression evaluator supporting + - * / ^ and parentheses
- Variable substitution in range expressions using {name} syntax
- Title/description variable substitution in expanded steps
Example use case: Towers of Hanoi formula where step count is 2^n-1
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The ephemeral proto path (collectDependenciesToSubgraph) was missing
waits_for handling that was already implemented in collectDependencies
for persisted protos. This ensures fanout gate dependencies are created
correctly for both ephemeral and persisted formula cooking.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add children-of(step-id) syntax for explicit spawner reference
- Add WaitsForSpec type and ParseWaitsFor() helper
- Update cook.go to create DepWaitsFor dependencies with metadata
- Infer spawner from first needs entry when using all-children
- Add validation tests for children-of() syntax
- Add unit tests for ParseWaitsFor()
This completes the Christmas Ornament aggregation pattern:
- survey-workers does for-each → creates N children
- aggregate waits-for children-of(survey-workers)
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Major refactor of molecular chemistry to make protos ephemeral:
- Formulas are now cooked directly to in-memory TemplateSubgraph
- No more proto beads stored in the database
Changes:
- cook.go: Add cookFormulaToSubgraph() and resolveAndCookFormula()
for in-memory formula cooking
- template.go: Add VarDefs field to TemplateSubgraph for default
value handling, add extractRequiredVariables() and
applyVariableDefaults() helpers
- pour.go: Try formula loading first for any name (not just mol-)
- wisp.go: Same pattern as pour
- mol_bond.go: Use resolveOrCookToSubgraph() for in-memory subgraphs
- mol_catalog.go: List formulas from disk instead of DB proto beads
- mol_distill.go: Output .formula.json files instead of proto beads
Flow: Formula (.formula.json) -> pour/wisp (cook inline) -> Mol/Wisp
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove resolvePartialIDDirect function and context import that became
dead code after switching to resolveOrCookFormula in bd-rciw.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Changes:
- bd cook: outputs proto JSON to stdout by default, add --persist flag
for legacy behavior (write to database)
- bd pour: accepts formula names, cooks inline as ephemeral proto,
spawns mol, then cleans up temporary proto
- bd wisp create: accepts formula names, cooks inline as ephemeral proto,
creates wisp, then cleans up temporary proto
- bd mol bond: already supported ephemeral protos (gt-8tmz.25)
The ephemeral proto pattern avoids persisting templates in the database.
Protos are only needed temporarily during spawn operations - the spawned
mol/wisp is what gets persisted.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- ApplyBranches and ApplyGates now clone steps before modifying,
matching the immutability pattern of ApplyLoops and ApplyAdvice
- Added internal applyBranchesWithMap/applyGatesWithMap for efficiency
- ApplyControlFlow builds stepMap once for both (gt-gpgdv optimization)
- Added cloneStepsRecursive helper
- Added TestApplyBranches_Immutability and TestApplyGates_Immutability
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fixes from review of gt-8tmz.25 implementation:
1. Dry-run no longer cooks formulas - added resolveOrDescribe() for
dry-run mode that checks if operand exists without cooking
2. Ephemeral protos now cleaned up after successful bond, not just
on error
3. Unique proto IDs to avoid collision - ephemeral protos use format
"_ephemeral-<formula>-<timestamp>" instead of formula name
4. Removed unused vars parameter from resolveOrCookFormula
5. Added informative output showing formulas will be cooked and
cleaned up
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Comprehensive changelog entries for all changes since v0.36.0:
- 8 new features (control flow, aspects, stale detection, etc.)
- 3 breaking changes (YAML→JSON, wisp architecture, mol run removal)
- 13 bug fixes
- 2 documentation updates
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Bond command now accepts formula names (e.g., mol-polecat-arm) in addition
to issue IDs. When a formula name is given:
1. Looks up the formula using formula.Parser
2. Resolves inheritance and applies transformations (control flow, advice,
expansions, aspects)
3. Cooks the formula inline to create an ephemeral proto
4. Uses the cooked proto for bonding
This eliminates the need for pre-cooked proto beads in the database,
enabling more dynamic workflow composition.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fixes a bug where outer iteration chaining was lost when nested loops
were expanded. The problem was:
1. chainLoopIterations set: outer.iter2.inner depends on outer.iter1.inner
2. ApplyLoops recursively expanded nested loops
3. outer.iter2.inner became outer.iter2.inner.iter1.work, etc.
4. The dependency was lost (referenced non-existent ID)
The fix:
- Move recursive ApplyLoops BEFORE chaining
- Add chainExpandedIterations that finds iteration boundaries by ID prefix
- Works with variable step counts per iteration (nested loops expand differently)
Now outer.iter2's first step correctly depends on outer.iter1's LAST step,
ensuring sequential execution of outer iterations.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add SourceFormula and SourceLocation fields to track where each step
came from during the cooking process. This enables debugging of complex
compositions with inheritance, expansion, and advice.
Changes:
- Added SourceFormula and SourceLocation fields to Step struct (formula/types.go)
- Added same fields to Issue struct (types/types.go)
- Added SetSourceInfo() to parser.go - sets source on all steps after parsing
- Updated cook.go to copy source fields from Step to Issue
- Updated dry-run output to display source info: [from: formula@location]
- Updated advice.go to set source on advice-generated steps
- Updated controlflow.go to preserve source on loop-expanded steps
- Updated expand.go to preserve source on template-expanded steps
The source location format is:
- steps[N] - regular step at index N
- steps[N].children[M] - child step
- steps[N].loop.body[M] - loop body step
- template[N] - expansion template step
- advice - step inserted by advice transformation
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Enables loops within loop bodies to be properly expanded:
- Copy Loop field in expandLoopIteration (was intentionally omitted)
- Add cloneLoopSpec for deep copying of LoopSpec with body steps
- Recursively call ApplyLoops at end of expandLoop to expand nested loops
- Also copy OnComplete field for consistency
Nested IDs follow natural chaining pattern:
outer.iter1.inner.iter2.step
Tested with 2-level and 3-level nesting scenarios.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Replace beads-metadata with beads-sync throughout docs
(matches code default and internal examples)
- Fix bd daemon start → bd daemon --start (correct flag syntax)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Claude Code's installed_plugins.json changed from v1 (plugins as structs)
to v2 (plugins as arrays). Update GetClaudePluginVersion() to handle both.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements the schema and validation for runtime dynamic expansion:
- Add OnCompleteSpec type for step completion triggers
- Add on_complete field to Step struct
- Validate for_each path format (must start with "output.")
- Validate bond is required with for_each (and vice versa)
- Validate parallel and sequential are mutually exclusive
- Add cloneOnComplete for proper step cloning
- Add comprehensive tests for parsing and validation
The runtime executor (in gastown) will interpret these fields to:
- Bond N molecules when step completes based on output.collection
- Run bonded molecules in parallel or sequential order
- Pass item/index context via vars substitution
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Critical bug fixes identified during code review:
1. External dependency rewriting: Dependencies on steps OUTSIDE the loop
are now preserved as-is instead of being incorrectly prefixed.
2. Children dependency rewriting: Child step dependencies are now properly
rewritten with iteration context.
3. Missing fields: Added Expand, ExpandVars, Gate fields to loop expansion.
4. Condition validation: Loop `until` conditions are now validated with
ParseCondition to catch syntax errors early.
5. Label format: Changed gate and loop labels from colon-delimited to
JSON format for unambiguous parsing:
- gate:{"condition":"expr"}
- loop:{"until":"expr","max":N}
Added TestApplyLoops_ExternalDependencies to verify the fix.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add loop, branch, and gate operators for formula step transformation:
- LoopSpec: Fixed-count loops expand body N times with chained iterations.
Conditional loops expand once with runtime metadata labels.
- BranchRule: Fork-join patterns wire dependencies for parallel paths.
- GateRule: Adds condition labels for runtime evaluation before steps.
Types added to types.go:
- LoopSpec (count/until/max/body)
- BranchRule (from/steps/join)
- GateRule (before/condition)
- Loop field on Step
- Branch/Gate arrays on ComposeRules
New controlflow.go with ApplyLoops, ApplyBranches, ApplyGates, and
ApplyControlFlow convenience function. Wired into cook.go before
advice and expansion operators.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Users who want manual control over git commits can now set:
bd config set no-git-ops true
This makes `bd prime` output the stealth-mode session close protocol
(just `bd sync --flush-only`) instead of the full git add/commit/push
workflow. Useful when:
- You want to verify work before committing
- Claude tries to auto-commit after context compaction
- You have a custom git workflow
The --stealth flag still works as before for one-off use.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
On Windows, running `bd init` outside a git repository could hang
indefinitely because git.IsWorktree() runs `git rev-parse --git-dir`
which may hang on Windows when not in a git repo.
The fix adds an isGitRepo() check before calling git.IsWorktree() in
both the main init flow and the checkExistingBeadsData helper.
Regression introduced in e01b7412 (Git worktree compatibility).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
GH#740: bd doctor --fix was auto-removing child→parent dependencies,
calling them an 'anti-pattern'. While these often indicate modeling
mistakes (deadlock), they may be intentional in some workflows.
Changes:
- Add --fix-child-parent flag (required to remove child→parent deps)
- Remove ChildParentDependencies from default --fix set
- Update warning message to reference new flag
- Update comments to reflect more nuanced understanding
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Empty set 'all' returns false (avoids premature gate passing)
- Add proper error handling for Atoi in count comparisons
- Extract inline regex to package-level var (performance)
- Handle == and != in compareString function
- Add nil/bool value handling in compare function
- Add tests for edge cases: empty children, nil output, bool values
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace fmt.Fprintf(os.Stderr, ...) + os.Exit(1) patterns with
FatalErrorRespectJSON() in updateCmd, closeCmd, and editCmd.
This ensures that when --json flag is set, errors are returned as
JSON objects ({"error": "message"}) instead of plain text.
Fixes: bd-28sq.1
Extends bd doctor to detect complete-but-unclosed molecules (epics where
all children are closed but root is still open).
- Added CheckStaleMolecules() to doctor/maintenance.go
- Added resolveBeadsDir() helper to follow Gas Town redirect files
- Check appears in Maintenance category with warning severity
- Shows example IDs and suggests 'bd mol stale' for review
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements formula management commands:
- bd formula list: Lists formulas from all search paths
- bd formula show <name>: Shows formula details, steps, composition rules
Search paths in priority order:
1. .beads/formulas/ (project)
2. ~/.beads/formulas/ (user)
3. ~/gt/.beads/formulas/ (town)
Features:
- Type filtering (--type workflow|expansion|aspect)
- JSON output support (--json)
- Shows variables, steps, advice, bond points, and aspects
- Formulas in earlier paths shadow later ones
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements command to find epics/molecules where all children are closed
but the root is still open. Helps identify work that's done but not
formally closed.
Flags:
--blocking Only show molecules blocking other work
--unassigned Only show unassigned molecules
--all Include molecules with 0 children
--json Machine-readable output
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
ApplyAdvice now collects original step IDs before applying rules and
only matches steps in that set. This prevents advice patterns (like "*")
from matching their own inserted before/after steps.
Added test case demonstrating that a "*" pattern only adds advice to
original steps, not to inserted steps.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
