- bd repo add/remove now writes to .beads/config.yaml instead of database
- bd repo remove deletes hydrated issues from the removed repo
- Added internal/config/repos.go for YAML config manipulation
- Added DeleteIssuesBySourceRepo for cleanup on remove
Fixes config disconnect where bd repo add wrote to DB but hydration read from YAML.
Breaking change: bd repo add no longer accepts optional alias argument.
Co-authored-by: Dylan Conlin <dylan.conlin@gmail.com>
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(doctor): UX improvements for diagnostics and daemon
- Add Repo Fingerprint check to detect when database belongs to a
different repository (copied .beads dir or git remote URL change)
- Add interactive fix for repo fingerprint with options: update repo ID,
reinitialize database, or skip
- Add visible warning when daemon takes >5s to start, recommending
'bd doctor' for diagnosis
- Detect install method (Homebrew vs script) and show only relevant
upgrade command
- Improve WARNINGS section:
- Add icons (⚠ or ✖) next to each item
- Color numbers by severity (yellow for warnings, red for errors)
- Render entire error lines in red
- Sort by severity (errors first)
- Fix alignment with checkmarks above
- Use heavier fail icon (✖) for better visibility
- Add integration and validation tests for doctor fixes
* fix(lint): address errcheck and gosec warnings
- mol_bond.go: explicitly ignore ephStore.Close() error
- beads.go: add nosec for .gitignore file permissions (0644 is standard)
Previously, bd repo commands (list, add, remove, sync) failed with
'unexpected end of JSON input' when repos.additional config key
had an empty value. GetConfig() returns ('', nil) for missing keys,
and json.Unmarshal fails on empty strings.
Added empty value check before JSON parsing to return empty map
in this case. Added tests for repo config helper functions.
DeepWiki provides up-to-date documentation people can talk to, for every public repo in the world (after being added to it's index). Adding this badge to a repository Readme tells DeepWiki to refresh it's docs automatically.
The DeepWiki link for Beads is
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Implements wisp management commands for ephemeral molecules:
- bd wisp list: List wisps with stale detection
- bd wisp gc: Garbage collect orphaned wisps
- bd mol burn: Delete wisp without creating digest
Wisps are ephemeral molecules stored in .beads-wisp/ for patrol cycles
and operational loops that shouldn't accumulate in permanent storage.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add wisp detection in mol squash: checks wisp storage if not in main
- squashWispToPermanent: creates digest in permanent, deletes from wisp
- Fix directory naming: .beads-wisps → .beads-wisp (singular, matches doc)
- Add comprehensive tests for wisp squash scenarios
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Standardize terminology for ephemeral molecule storage:
- .beads-ephemeral/ → .beads-wisps/
- --ephemeral flag → --wisp flag
- All Ephemeral* functions → Wisp*
Wisps are the "steam" in Gas Town's engine metaphor - ephemeral
molecules that evaporate after squash.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When --ephemeral is set:
- Spawned molecules go to .beads-ephemeral/ instead of .beads/
- Ephemeral directory is automatically gitignored
- No auto-flush (ephemeral does not sync)
- Proto+proto bonding ignores flag (templates stay in permanent storage)
Updated help text to document wisp workflow (bond then squash/burn).
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add .beads-ephemeral/ storage support for ephemeral molecule tracking:
- FindEphemeralDir: locate ephemeral directory (sibling to .beads/)
- FindEphemeralDatabasePath: get DB path, create directory if needed
- NewEphemeralStorage: open ephemeral SQLite database
- EnsureEphemeralGitignore: add .beads-ephemeral/ to .gitignore
- IsEphemeralDatabase: check if a path is ephemeral storage
Part of the wisp storage epic for Gas Town patrol cycles.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
GetReadyWork now lazily resolves external dependencies at query time:
- External refs (external:project:capability) checked against target DB
- Issues with unsatisfied external deps are filtered from ready list
- Satisfaction = closed issue with provides:<capability> label in target
Key changes:
- Remove FK constraint on depends_on_id to allow external refs
- Add migration 025 to drop FK and recreate views
- Filter external deps in GetReadyWork, not in blocked_issues_cache
- Add application-level validation for orphaned local deps
- Comprehensive tests for external dep resolution
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- bd ship <capability> finds issue with export:<capability> label
- Validates issue is closed (or --force to override)
- Adds provides:<capability> label to mark capability as shipped
- Protects provides:* namespace in bd label add
- Supports --dry-run for preview
External projects depend on capabilities via:
bd dep add <issue> external:<project>:<capability>
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Config (bd-66w1):
- Add external_projects config for mapping project names to paths
- Add GetExternalProjects() and ResolveExternalProjectPath() functions
- Add config documentation and tests
External deps (bd-om4a):
- bd dep add accepts external:project:capability syntax
- External refs stored as-is in dependencies table
- GetBlockedIssues includes external deps in blocked_by list
- blocked_issues_cache includes external dependencies
- Add validation and parsing helpers for external refs
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The code assumed rootID was at least 8 chars, but issue IDs
like 'gt-i4lo' are only 7 chars (prefix-hash format).
Simply use the full ID instead of truncating - IDs are already
short enough for display.
- Add CheckOrphanedIssues to detect issues referenced in commits but still open
- Pattern matches (prefix-xxx) in git log against open issues in database
- Reports warning with issue IDs and commit hashes
- Add 8 comprehensive tests for the new check
Also:
- Add tests for mol spawn --attach functionality (bd-f7p1)
- Document commit message convention in AGENT_INSTRUCTIONS.md
- Fix CheckpointWAL to use wrapDBError for consistency
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The --as flag description correctly says "Custom title" but the variable
was named customID and dry-run output said "Custom ID". Fixed for consistency:
- Renamed variable customID -> customTitle
- Changed dry-run output from "Custom ID" to "Custom title"
Closes bd-e7ou
Document that wisps are intentionally local-only and use hard delete
instead of tombstones. This is by design - wisps never sync to other
clones, so tombstones are unnecessary overhead.
Closes bd-4bsb
GetConfig() returns ("", nil) for missing/empty config keys.
getRepoConfig() then tried json.Unmarshal([]byte(""), ...) which
fails with "unexpected end of JSON input".
Add empty value check before JSON parsing - return empty map when
config value is empty string.
Closes GH#680
Co-Authored-By: dylan-conlin <dylan-conlin@users.noreply.github.com>
