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fix: Allow tombstones to retain closed_at timestamp

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Previously, tombstones could not have a closed_at timestamp due to:
1. Go validation: `if status != closed && closed_at != nil` failed
2. SQL CHECK constraint: `(status = 'closed') = (closed_at IS NOT NULL)`

This caused import failures for tombstones that were closed before being
deleted - a valid scenario where we want to preserve the historical
closed_at timestamp for audit purposes.

Changes:
- internal/types/types.go: Updated validation to allow tombstones with
  closed_at (line 253)
- internal/storage/sqlite/schema.go: Updated CHECK constraint to allow
  closed AND tombstone statuses to have closed_at
- internal/storage/sqlite/migrations/028_tombstone_closed_at.go: Migration
  to update existing databases with the new constraint
- .beads/issues.jsonl: Fixed bd-6s61 status from 'closed' to 'tombstone'

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Steve Yegge
2025-12-26 00:57:59 -08:00
parent 9dc0da9fdd
commit 64d2f372a3
7 changed files with 184 additions and 1687 deletions
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2
.beads/issues.jsonl
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@@ -104,7 +104,7 @@
{"id":"bd-6ns7","title":"test hook pin","status":"tombstone","priority":2,"issue_type":"task","assignee":"stevey","created_at":"2025-12-23T04:39:16.619755-08:00","updated_at":"2025-12-23T04:51:29.436788-08:00","deleted_at":"2025-12-23T04:51:29.436788-08:00","deleted_by":"daemon","delete_reason":"delete","original_type":"task"}
{"id":"bd-6pc","title":"Implement bd pin/unpin commands","description":"Add 'bd pin \u003cid\u003e' and 'bd unpin \u003cid\u003e' commands to toggle the pinned status of issues. Should support multiple IDs like other bd commands.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-18T23:33:28.292937-08:00","updated_at":"2025-12-19T17:43:35.713398-08:00","closed_at":"2025-12-19T00:35:31.612589-08:00","dependencies":[{"issue_id":"bd-6pc","depends_on_id":"bd-0vg","type":"blocks","created_at":"2025-12-18T23:33:56.119852-08:00","created_by":"daemon"},{"issue_id":"bd-6pc","depends_on_id":"bd-7h5","type":"blocks","created_at":"2025-12-18T23:34:07.352848-08:00","created_by":"daemon"}]}
{"id":"bd-6rl","title":"Merge3Way public API does not expose TTL parameter","description":"The public Merge3Way() function in merge.go does not allow callers to configure the tombstone TTL. It hard-codes the default via merge3WayWithTTL(). While merge3WayWithTTL() exists, it is unexported (lowercase). This means the CLI and tests cannot configure TTL at merge time. Use cases: testing with different TTL values, per-repository TTL configuration, debugging with short TTL, supporting --ttl flag in bd merge command (mentioned in design doc bd-zvg). Recommendation: Export Merge3WayWithTTL (rename to uppercase). Files: internal/merge/merge.go:77, 292-298","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-12-05T16:36:15.756814-08:00","updated_at":"2025-12-25T22:45:32.157938-08:00","closed_at":"2025-12-25T22:45:32.157938-08:00","close_reason":"Closed"}
{"id":"bd-6s61","title":"Version Bump: {{version}}","description":"Release checklist for version {{version}}. This molecule ensures all release steps are completed properly.","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-12-19T22:55:42.487701-08:00","updated_at":"2025-12-25T13:27:50.789625-08:00","closed_at":"2025-12-25T13:27:50.789625-08:00","close_reason":"All children completed","labels":["molecule","template"],"deleted_at":"2025-12-24T16:25:31.251346-08:00","deleted_by":"daemon","delete_reason":"delete","original_type":"epic"}
{"id":"bd-6s61","title":"Version Bump: {{version}}","description":"Release checklist for version {{version}}. This molecule ensures all release steps are completed properly.","status":"tombstone","priority":1,"issue_type":"epic","created_at":"2025-12-19T22:55:42.487701-08:00","updated_at":"2025-12-25T13:27:50.789625-08:00","closed_at":"2025-12-25T13:27:50.789625-08:00","close_reason":"All children completed","labels":["molecule","template"],"deleted_at":"2025-12-24T16:25:31.251346-08:00","deleted_by":"daemon","delete_reason":"delete","original_type":"epic"}
{"id":"bd-6sm6","title":"Improve test coverage for internal/export (37.1% → 60%)","description":"The export package has only 37.1% test coverage. Export functionality needs good coverage to ensure data integrity.\n\nCurrent coverage: 37.1%\nTarget coverage: 60%","status":"closed","priority":2,"issue_type":"task","assignee":"beads/alpha","created_at":"2025-12-13T20:43:06.802277-08:00","updated_at":"2025-12-23T22:32:29.16846-08:00","closed_at":"2025-12-23T22:32:29.16846-08:00","close_reason":"Coverage already at 71.8% (target was 60%). Recent commits ba8beb53 and e3e0a044 added tests."}
{"id":"bd-6ss","title":"Improve test coverage","description":"The test suite reports less than 45% code coverage. Identify the specific uncovered areas of the codebase, including modules, functions, or features. Rank them by potential impact on system reliability and business value, from most to least, and provide actionable recommendations for improving coverage in each area.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-18T06:54:23.036822442-07:00","updated_at":"2025-12-18T07:17:49.245940799-07:00","closed_at":"2025-12-18T07:17:49.245940799-07:00"}
{"id":"bd-70an","title":"test pin","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-21T11:19:16.760214-08:00","updated_at":"2025-12-21T11:19:46.500688-08:00","closed_at":"2025-12-21T11:19:46.500688-08:00","close_reason":"test issue for pin fix"}

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1
internal/storage/sqlite/migrations.go
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@@ -44,6 +44,7 @@ var migrationsList = []Migration{
{"remove_depends_on_fk", migrations.MigrateRemoveDependsOnFK},
{"additional_indexes", migrations.MigrateAdditionalIndexes},
{"gate_columns", migrations.MigrateGateColumns},
{"tombstone_closed_at", migrations.MigrateTombstoneClosedAt},
}
// MigrationInfo contains metadata about a migration for inspection

174
internal/storage/sqlite/migrations/028_tombstone_closed_at.go Normal file
View File

@@ -0,0 +1,174 @@
package migrations
import (
"database/sql"
"fmt"
)
// MigrateTombstoneClosedAt updates the closed_at constraint to allow tombstones
// to retain their closed_at timestamp from before deletion.
//
// Previously: CHECK ((status = 'closed') = (closed_at IS NOT NULL))
// - This required clearing closed_at when creating tombstones from closed issues
//
// Now: CHECK (closed + tombstone OR non-closed/tombstone with no closed_at)
// - closed issues must have closed_at
// - tombstones may have closed_at (from before deletion) or not
// - other statuses must NOT have closed_at
//
// This allows importing tombstones that were closed before being deleted,
// preserving the historical closed_at timestamp for audit purposes.
func MigrateTombstoneClosedAt(db *sql.DB) error {
// SQLite doesn't support ALTER TABLE to modify CHECK constraints
// We must recreate the table with the new constraint
// Step 0: Drop views that depend on the issues table
_, err := db.Exec(`DROP VIEW IF EXISTS ready_issues`)
if err != nil {
return fmt.Errorf("failed to drop ready_issues view: %w", err)
}
_, err = db.Exec(`DROP VIEW IF EXISTS blocked_issues`)
if err != nil {
return fmt.Errorf("failed to drop blocked_issues view: %w", err)
}
// Step 1: Create new table with updated constraint
_, err = db.Exec(`
CREATE TABLE IF NOT EXISTS issues_new (
id TEXT PRIMARY KEY,
content_hash TEXT,
title TEXT NOT NULL CHECK(length(title) <= 500),
description TEXT NOT NULL DEFAULT '',
design TEXT NOT NULL DEFAULT '',
acceptance_criteria TEXT NOT NULL DEFAULT '',
notes TEXT NOT NULL DEFAULT '',
status TEXT NOT NULL DEFAULT 'open',
priority INTEGER NOT NULL DEFAULT 2 CHECK(priority >= 0 AND priority <= 4),
issue_type TEXT NOT NULL DEFAULT 'task',
assignee TEXT,
estimated_minutes INTEGER,
created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
closed_at DATETIME,
external_ref TEXT,
source_repo TEXT DEFAULT '',
compaction_level INTEGER DEFAULT 0,
compacted_at DATETIME,
compacted_at_commit TEXT,
original_size INTEGER,
deleted_at DATETIME,
deleted_by TEXT DEFAULT '',
delete_reason TEXT DEFAULT '',
original_type TEXT DEFAULT '',
sender TEXT DEFAULT '',
ephemeral INTEGER DEFAULT 0,
close_reason TEXT DEFAULT '',
pinned INTEGER DEFAULT 0,
is_template INTEGER DEFAULT 0,
await_type TEXT,
await_id TEXT,
timeout_ns INTEGER,
waiters TEXT,
CHECK (
(status = 'closed' AND closed_at IS NOT NULL) OR
(status = 'tombstone') OR
(status NOT IN ('closed', 'tombstone') AND closed_at IS NULL)
)
)
`)
if err != nil {
return fmt.Errorf("failed to create new issues table: %w", err)
}
// Step 2: Copy data from old table to new table
_, err = db.Exec(`
INSERT INTO issues_new
SELECT * FROM issues
`)
if err != nil {
return fmt.Errorf("failed to copy issues data: %w", err)
}
// Step 3: Drop old table
_, err = db.Exec(`DROP TABLE issues`)
if err != nil {
return fmt.Errorf("failed to drop old issues table: %w", err)
}
// Step 4: Rename new table to original name
_, err = db.Exec(`ALTER TABLE issues_new RENAME TO issues`)
if err != nil {
return fmt.Errorf("failed to rename new issues table: %w", err)
}
// Step 5: Recreate indexes (they were dropped with the table)
indexes := []string{
`CREATE INDEX IF NOT EXISTS idx_issues_status ON issues(status)`,
`CREATE INDEX IF NOT EXISTS idx_issues_priority ON issues(priority)`,
`CREATE INDEX IF NOT EXISTS idx_issues_assignee ON issues(assignee)`,
`CREATE INDEX IF NOT EXISTS idx_issues_created_at ON issues(created_at)`,
`CREATE INDEX IF NOT EXISTS idx_issues_external_ref ON issues(external_ref) WHERE external_ref IS NOT NULL`,
`CREATE INDEX IF NOT EXISTS idx_issues_pinned ON issues(pinned) WHERE pinned = 1`,
`CREATE INDEX IF NOT EXISTS idx_issues_is_template ON issues(is_template) WHERE is_template = 1`,
`CREATE INDEX IF NOT EXISTS idx_issues_updated_at ON issues(updated_at)`,
`CREATE INDEX IF NOT EXISTS idx_issues_status_priority ON issues(status, priority)`,
`CREATE INDEX IF NOT EXISTS idx_issues_gate ON issues(issue_type) WHERE issue_type = 'gate'`,
}
for _, idx := range indexes {
if _, err := db.Exec(idx); err != nil {
return fmt.Errorf("failed to create index: %w", err)
}
}
// Step 6: Recreate views that we dropped
_, err = db.Exec(`
CREATE VIEW IF NOT EXISTS ready_issues AS
WITH RECURSIVE
blocked_directly AS (
SELECT DISTINCT d.issue_id
FROM dependencies d
JOIN issues blocker ON d.depends_on_id = blocker.id
WHERE d.type = 'blocks'
AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred')
),
blocked_transitively AS (
SELECT issue_id, 0 as depth
FROM blocked_directly
UNION ALL
SELECT d.issue_id, bt.depth + 1
FROM blocked_transitively bt
JOIN dependencies d ON d.depends_on_id = bt.issue_id
WHERE d.type = 'parent-child'
AND bt.depth < 50
)
SELECT i.*
FROM issues i
WHERE i.status = 'open'
AND NOT EXISTS (
SELECT 1 FROM blocked_transitively WHERE issue_id = i.id
)
`)
if err != nil {
return fmt.Errorf("failed to recreate ready_issues view: %w", err)
}
_, err = db.Exec(`
CREATE VIEW IF NOT EXISTS blocked_issues AS
SELECT
i.*,
COUNT(d.depends_on_id) as blocked_by_count
FROM issues i
JOIN dependencies d ON i.id = d.issue_id
JOIN issues blocker ON d.depends_on_id = blocker.id
WHERE i.status IN ('open', 'in_progress', 'blocked', 'deferred')
AND d.type = 'blocks'
AND blocker.status IN ('open', 'in_progress', 'blocked', 'deferred')
GROUP BY i.id
`)
if err != nil {
return fmt.Errorf("failed to recreate blocked_issues view: %w", err)
}
return nil
}

7
internal/storage/sqlite/schema.go
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@@ -36,7 +36,12 @@ CREATE TABLE IF NOT EXISTS issues (
is_template INTEGER DEFAULT 0,
-- NOTE: replies_to, relates_to, duplicate_of, superseded_by removed per Decision 004
-- These relationships are now stored in the dependencies table
CHECK ((status = 'closed') = (closed_at IS NOT NULL))
-- closed_at constraint: closed issues must have it, tombstones may retain it from before deletion
CHECK (
(status = 'closed' AND closed_at IS NOT NULL) OR
(status = 'tombstone') OR
(status NOT IN ('closed', 'tombstone') AND closed_at IS NULL)
)
);
CREATE INDEX IF NOT EXISTS idx_issues_status ON issues(status);

3
internal/types/types.go
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@@ -246,10 +246,11 @@ func (i *Issue) ValidateWithCustomStatuses(customStatuses []string) error {
return fmt.Errorf("estimated_minutes cannot be negative")
}
// Enforce closed_at invariant: closed_at should be set if and only if status is closed
// Exception: tombstones may retain closed_at from before deletion
if i.Status == StatusClosed && i.ClosedAt == nil {
return fmt.Errorf("closed issues must have closed_at timestamp")
}
if i.Status != StatusClosed && i.ClosedAt != nil {
if i.Status != StatusClosed && i.Status != StatusTombstone && i.ClosedAt != nil {
return fmt.Errorf("non-closed issues cannot have closed_at timestamp")
}
// Enforce tombstone invariants (bd-md2): deleted_at must be set for tombstones, and only for tombstones