Steve Yegge aff38708e0 fix: bd doctor false positive for molecule/wisp prefix variants ...

The prefix mismatch check in bd doctor was reporting warnings when
issues were created via molecule workflows (bd mol pour), which
intentionally use a different prefix pattern (<base>-mol instead
of just <base>).

Added recognition of valid workflow prefix variants:
- <prefix>-mol (molecules from bd mol pour)
- <prefix>-wisp (ephemeral wisps)
- <prefix>-eph (ephemeral issues)

These are intentional prefix extensions for visual distinction, not
actual mismatches. The check now only warns for truly mismatched
prefixes (e.g., different project entirely).

Added comprehensive regression tests for all prefix variant cases.

Fixes #811

Generated with Claude Code

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2025-12-30 17:43:47 -08:00

..

doctor

fix: bd doctor false positive for molecule/wisp prefix variants

2025-12-30 17:43:47 -08:00

setup

fix: resolve lint errors blocking CI

2025-12-29 15:58:24 -08:00

templates/hooks

feat: add prepare-commit-msg hook for agent identity trailers (bd-luso)

2025-12-29 21:26:32 -08:00

testdata

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.gitattributes

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@AGENTS.md

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activity_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

activity.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

admin_aliases.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

admin.go

feat: add bd admin parent command for cleanup/compact/reset (bd-3u8m)

2025-12-27 16:21:08 -08:00

agent_test.go

feat: add bd agent state command for ZFC-compliant state reporting (bd-uxlb)

2025-12-28 01:56:53 -08:00

agent.go

feat: add structured labels for agent beads (bd-g7eq)

2025-12-29 21:15:46 -08:00

AGENTS.md

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audit.go

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autoflush.go

refactor: Break up 280-line flushToJSONLWithState into focused helpers (bd-9hc9)

2025-12-28 16:23:45 -08:00

autoimport_test.go

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autoimport.go

Add debug logging for YAML parse errors in autoimport (bd-mql4)

2025-12-30 16:51:14 -08:00

autostart_test.go

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cleanup.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

cli_coverage_show_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

cli_fast_test.go

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close.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

comments_test.go

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comments.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

compact_rpc.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

compact_test.go

feat(compact): Add --prune mode for standalone tombstone pruning (bd-c7y5)

2025-12-24 00:08:10 -08:00

compact_tombstone.go

fix: bd admin compact --older-than=0 now expires all tombstones

2025-12-30 00:00:25 -08:00

compact.go

fix: bd admin compact --older-than=0 now expires all tombstones

2025-12-30 00:00:25 -08:00

config_test.go

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config.go

fix: Show warning when config.yaml overrides database config (bd-20j)

2025-12-29 14:03:39 -08:00

context.go

Refactor: Introduce CommandContext to consolidate global variables (bd-qobn)

2025-12-30 16:29:28 -08:00

cook_test.go

feat: Compile-time vs runtime cooking (gt-8tmz.23)

2025-12-25 18:40:15 -08:00

cook.go

fix: --var flag now allows commas in values (#786)

2025-12-29 16:17:51 -08:00

count.go

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create_form_test.go

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create_form.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

create_test.go

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create.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

daemon_autoimport_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_autostart_unit_test.go

feat: auto-bypass daemon for wisp operations (bd-ta4r)

2025-12-28 02:11:13 -08:00

daemon_autostart.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_basics_test.go

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daemon_config.go

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daemon_crash_test.go

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daemon_debouncer_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_debouncer.go

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daemon_event_loop.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_health_freebsd.go

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daemon_health_solaris.go

fix: add illumos/solaris support for disk space check (#798)

2025-12-29 14:43:00 -08:00

daemon_health_unix.go

fix: add illumos/solaris support for disk space check (#798)

2025-12-29 14:43:00 -08:00

daemon_health_wasm.go

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daemon_health_windows.go

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daemon_integration_test.go

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daemon_lifecycle.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_local_test.go

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daemon_lock_test.go

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daemon_lock_unix.go

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daemon_lock_wasm.go

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daemon_lock_windows.go

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daemon_lock.go

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daemon_logger.go

chore: remove deprecated setupDaemonLoggerLegacy function (bd-2dwo)

2025-12-30 00:27:12 -08:00

daemon_parent_test.go

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daemon_rotation_test.go

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daemon_server.go

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daemon_sync_branch_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_sync_branch.go

fix: bd sync fails to copy local changes TO beads-sync worktree (#810)

2025-12-30 16:49:50 -08:00

daemon_sync_state.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemon_sync_test.go

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daemon_sync.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_test.go

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daemon_unix_test.go

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daemon_unix.go

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daemon_wasm.go

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daemon_watcher_platform_test.go

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daemon_watcher_test.go

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daemon_watcher.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

daemon_windows.go

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daemon.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

daemons_test.go

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daemons.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

defer.go

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delete_rpc_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

delete_test.go

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delete.go

fix: bd delete --cascade now recursively deletes dependents (#787)

2025-12-29 15:10:59 -08:00

deletion_tracking_test.go

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deletion_tracking.go

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dep_test.go

feat(deps): detect/prevent child→parent dependency anti-pattern (bd-nim5)

2025-12-24 13:03:27 -08:00

dep.go

feat: add refs field for cross-references with relationship types (bd-irah)

2025-12-30 15:52:33 -08:00

detect_pollution.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

direct_mode_test.go

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direct_mode.go

Refactor: Introduce CommandContext to consolidate global variables (bd-qobn)

2025-12-30 16:29:28 -08:00

docs.md

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doctor_fix.go

feat: Enhance bd doctor with force repair and source selection

2025-12-29 22:59:48 -08:00

doctor_health.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

doctor_pollution.go

fix: Add nolint comments for gosec/errcheck/unparam warnings

2025-12-29 14:39:43 -08:00

doctor_repair_chaos_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

doctor_repair_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

doctor_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

doctor.go

Merge pull request #805 from kraitsura/feature/bd-doctor-enhancements

2025-12-30 10:34:41 -08:00

duplicate.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

duplicates_test.go

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duplicates.go

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edit.go

fix: Add nolint comments for gosec/errcheck/unparam warnings

2025-12-29 14:39:43 -08:00

epic_test.go

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epic.go

fix: Use FatalErrorRespectJSON across all commands (bd-28sq)

2025-12-25 13:56:19 -08:00

errors.go

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export_import_test.go

Add close_reason to JSONL format documentation and tests (bd-lxzx)

2025-12-30 17:05:48 -08:00

export_integrity_integration_test.go

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export_mtime_test.go

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export_staleness_test.go

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export_test.go

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export.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

external_ref_test.go

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flags.go

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flush_manager_test.go

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flush_manager.go

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fork_protection_test.go

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fork_protection.go

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formula.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

gate.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

git_sync_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

git_test_helpers.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

graph_test.go

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graph.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

helpers_test.go

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hooks_test.go

Add unit tests to improve cmd/bd CLI coverage (bd-llfl)

2025-12-30 17:14:55 -08:00

hooks.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

human.go

Add bd human command for focused help menu

2025-12-29 14:33:19 -08:00

import_bug_test.go

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import_cancellation_test.go

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import_helpers_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

import_idempotent_test.go

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import_mtime_test.go

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import_multipart_id_test.go

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import_profile_test.go

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import_shared.go

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import_uncommitted_test.go

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import.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

info_test.go

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info.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

init_agent.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_contributor.go

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init_git_hooks.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_hooks_test.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

init_stealth.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_team.go

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init_templates.go

refactor: Split init.go from 1928 to 705 lines (bd-xtf5)

2025-12-28 18:43:09 -08:00

init_test.go

fix: remove gitignore negations that override fork protection (#796)

2025-12-29 14:52:29 -08:00

init.go

fix: prevent sync.branch from being set to main/master (#807)

2025-12-30 16:45:51 -08:00

integrity_content_test.go

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integrity_test.go

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integrity.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

jira_test.go

Implement Jira issue timestamp comparison for sync (bd-0qx5)

2025-12-30 16:07:31 -08:00

jira.go

Implement Jira issue timestamp comparison for sync (bd-0qx5)

2025-12-30 16:07:31 -08:00

jsonl_integrity_test.go

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label_test.go

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label.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

last_touched_test.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

last_touched.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

linear_conflict.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

linear_sync.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

linear_test.go

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linear.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

list_helpers_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

list_test.go

Add unit tests to improve cmd/bd CLI coverage (bd-llfl)

2025-12-30 17:14:55 -08:00

list.go

Add BD_AGENT_MODE for ultra-compact output

2025-12-30 16:04:39 -08:00

mail.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

main_daemon.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

main_errors.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

main_help.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

main_test.go

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main.go

Fix BD_ACTOR handling in direct mode paths

2025-12-30 16:51:14 -08:00

markdown_test.go

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markdown.go

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merge_security_test.go

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merge.go

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migrate_hash_ids_test.go

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migrate_hash_ids.go

feat: integrate migration detection into bd doctor (bd-7l27)

2025-12-30 00:06:42 -08:00

migrate_issues.go

feat: integrate migration detection into bd doctor (bd-7l27)

2025-12-30 00:06:42 -08:00

migrate_sync_test.go

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migrate_sync.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

migrate_test.go

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migrate_tombstones.go

feat: integrate migration detection into bd doctor (bd-7l27)

2025-12-30 00:06:42 -08:00

migrate.go

feat: integrate migration detection into bd doctor (bd-7l27)

2025-12-30 00:06:42 -08:00

mol_bond.go

fix: rename BondRef.ProtoID to SourceID for clarity (bd-ia3g)

2025-12-30 00:40:16 -08:00

mol_burn.go

feat: bd mol burn now works on mols, not just wisps (bd-l6yk)

2025-12-29 17:10:26 -08:00

mol_current.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

mol_distill.go

fix: --var flag now allows commas in values (#786)

2025-12-29 16:17:51 -08:00

mol_show.go

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mol_squash.go

refactor: remove Gas Town references from codebase

2025-12-30 14:13:32 -08:00

mol_stale.go

feat: add daemon RPC endpoints for config and mol stale (bd-ag35)

2025-12-30 06:59:51 -08:00

mol_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

mol.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

nodb_test.go

Refactor: Introduce CommandContext to consolidate global variables (bd-qobn)

2025-12-30 16:29:28 -08:00

nodb.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

onboard_test.go

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onboard.go

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orphans_test.go

test: improve nodb and orphans coverage

2025-12-29 14:17:44 -08:00

orphans.go

test: improve nodb and orphans coverage

2025-12-29 14:17:44 -08:00

output_test.go

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periodic_remote_sync_test.go

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pour.go

fix: --var flag now allows commas in values (#786)

2025-12-29 16:17:51 -08:00

prime_test.go

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prime.go

feat: show redirect info in bd prime output (bd-kblo)

2025-12-27 21:33:01 -08:00

quick.go

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quickstart.go

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readonly_test.go

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ready_test.go

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ready.go

feat: Add mol_type schema field for molecule type classification (bd-oxgi)

2025-12-28 19:52:51 -08:00

reinit_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

relate_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

relate.go

docs: Document deprecation timeline and add removal warnings (bd-pndo)

2025-12-28 16:40:43 -08:00

rename_prefix_repair_test.go

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rename_prefix_test.go

fix: remove arbitrary 8-char prefix limit from rename-prefix (GH#770)

2025-12-27 22:24:19 -08:00

rename_prefix.go

fix: remove arbitrary 8-char prefix limit from rename-prefix (GH#770)

2025-12-27 22:24:19 -08:00

reopen_test.go

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reopen.go

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repair_deps_test.go

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repair_orphans_test.go

feat: Add bd repair command for orphaned foreign key refs (hq-2cchm)

2025-12-29 12:43:22 -08:00

repair.go

fix: bd repair - consistent JSON error handling for find operations

2025-12-29 13:16:47 -08:00

repo.go

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reset_test.go

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reset.go

feat: add bd admin parent command for cleanup/compact/reset (bd-3u8m)

2025-12-27 16:21:08 -08:00

restore_test.go

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restore.go

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routed.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

sandbox_test.go

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sandbox_unix.go

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sandbox_windows.go

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scripttest_test.go

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search_test.go

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search.go

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setup.go

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ship.go

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show_thread.go

refactor: Split large cmd/bd files to meet 800-line limit (bd-xtf5)

2025-12-28 18:43:09 -08:00

show_unit_helpers_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

show_unit_helpers.go

Centralize validation patterns with composable validators (bd-jbqx)

2025-12-30 16:00:22 -08:00

show.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

simple_helpers_test.go

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slot.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

snapshot_manager.go

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stale_test.go

fix(json): audit and standardize JSON output across commands (bd-au0.7)

2025-12-24 00:10:14 -08:00

stale.go

fix(json): audit and standardize JSON output across commands (bd-au0.7)

2025-12-24 00:10:14 -08:00

staleness.go

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state_test.go

feat: add bd state and bd set-state helper commands (bd-7l67)

2025-12-30 15:57:08 -08:00

state.go

feat: add bd state and bd set-state helper commands (bd-7l67)

2025-12-30 15:57:08 -08:00

status_test.go

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status.go

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swarm.go

fix: Add nolint comments for gosec/errcheck/unparam warnings

2025-12-29 14:39:43 -08:00

sync_branch_priority_test.go

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sync_branch.go

fix: Prevent bd sync from committing non-.beads files (bd-trgb)

2025-12-25 12:05:46 -08:00

sync_check.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

sync_export.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

sync_git.go

fix: resolve lint errors blocking CI

2025-12-29 15:58:24 -08:00

sync_helpers_more_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

sync_import.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

sync_local_only_test.go

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sync_merge_test.go

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sync_test.go

Refactor TestZFCSkipsExportAfterImport to use direct import logic (bd-h048)

2025-12-30 16:05:15 -08:00

sync.go

Add sync branch integrity guards for force-push detection (bd-hlsw.4)

2025-12-30 17:07:25 -08:00

template_test.go

fix: mol run loads all hierarchical children + supports title lookup (bd-c8d5, bd-drcx)

2025-12-24 23:33:34 -08:00

template.go

fix: --var flag now allows commas in values (#786)

2025-12-29 16:17:51 -08:00

test_guard_helpers.go

test: add git helper and guard annotations

2025-12-28 20:48:37 -08:00

test_helpers_test.go

Refactor: Introduce CommandContext to consolidate global variables (bd-qobn)

2025-12-30 16:29:28 -08:00

test_repo_beads_guard_test.go

Refactor: Introduce CommandContext to consolidate global variables (bd-qobn)

2025-12-30 16:29:28 -08:00

test_wait_helper.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

thanks.go

refactor: relocate thanks command to bd info --thanks (bd-wb9g)

2025-12-27 16:08:34 -08:00

thread_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

tips_example_test.go

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tips_test.go

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tips.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

undefer.go

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update.go

Add 'last touched' issue tracking for update/close without ID

2025-12-30 16:58:10 -08:00

upgrade.go

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utils_unit_test.go

Add unit tests to improve cmd/bd CLI coverage (bd-llfl)

2025-12-30 17:14:55 -08:00

version_test.go

Refactor: Introduce CommandContext to consolidate global variables (bd-qobn)

2025-12-30 16:29:28 -08:00

version_tracking_test.go

Add unit tests to improve cmd/bd CLI coverage (bd-llfl)

2025-12-30 17:14:55 -08:00

version_tracking.go

chore: remove issue ID references from comments and changelogs

2025-12-28 10:05:16 -08:00

version.go

chore: Bump version to 0.41.0

2025-12-29 16:34:14 -08:00

where.go

feat: add 'bd where' command to show active beads location (bd-8x43)

2025-12-27 21:27:44 -08:00

wisp.go

fix: --var flag now allows commas in values (#786)

2025-12-29 16:17:51 -08:00

worktree_cmd.go

fix: Add nolint comments for gosec/errcheck/unparam warnings

2025-12-29 14:39:43 -08:00

worktree_daemon_test.go

refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

2025-12-27 16:02:15 -08:00

worktree_test.go

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worktree.go

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