Sanitized server-only runtime evidence — issue 25289
Visual matrix: empty, confirmed by lead proof-audit. Proof: prior red test + actual runtime transcript.
No server or browser was started during evidence assembly. No source was changed.

Base/main: [0a3b561bc0](https://git.cafe/pingdotgg/t3code/commit/0a3b561bc0901d8fa47e430fc9d8593918cde978)
Fix head: [d511961ca4](https://git.cafe/pingdotgg/t3code/commit/d511961ca4d815066b2a979270a77a1698d72181)

BEFORE — supplied lead capture (not rerun during assembly)
Issue 25289: preview migration collision
Environment: fs-11, Linux x86_64, Node 26.12.1; isolated checkout /home/ubuntu/wt/issue-25289
Before: main [0a3b561bc0](https://git.cafe/pingdotgg/t3code/commit/0a3b561bc0901d8fa47e430fc9d8593918cde978)

Read-only source history (SELECT migration_id,name FROM effect_sql_migrations WHERE migration_id>=65):
65 CodexUsageNativeTurnIndex
66 RepairClientSettlementTimestamps
67 WebhookDedupe
68 PeerLinks
69 PeerLinkFence
70 WaitingLinkRequestIndex

Attempt 1: vp run migrate-dev-db
Source opened read-only; snapshot copied under worktree .t3/userdata.
Result: MigrateDevDbPhaseError during migrate, caused by:
MigrationError: This database's migration history would skip required schema migrations: 68_ShellStopRequestIndex (recorded: PeerLinks), 69_ThreadMessageSearch (recorded: PeerLinkFence). The migrator skips every id up to the highest recorded id (70), regardless of name.

Attempt 2: SQLite backup API copied source opened with mode=ro into worktree .t3/userdata/statev2.sqlite; vp run dev --no-seed
[dev-runner] mode=dev source=worktree serverPort=15602 webPort=7562 baseDir=/home/ubuntu/wt/issue-25289/.t3
Vite ready. Server startup failed:
[03:48:17.187] ERROR (#2): MigrationError: This database's migration history would skip required schema migrations: 68_ShellStopRequestIndex (recorded: PeerLinks), 69_ThreadMessageSearch (recorded: PeerLinkFence). The migrator skips every id up to the highest recorded id (70), regardless of name.
at assertV2MigrationsCanRun
at runMigrations
at server.runServerCommand
Failed running 'src/bin.ts'. Waiting for file changes before restarting...
Stopped the spawned dev runner with Ctrl-C. No server reached ready state.

Red test (commit [e06dfa6a90](https://git.cafe/pingdotgg/t3code/commit/e06dfa6a9015490699c01143c02ccf1c40e769af)):
vp test run src/persistence/Migrations.test.ts (from apps/server)
1 failed, 7 passed. Failure: same MigrationError at Migrations.ts:189.
Test: upgrades a 0.1.2-preview.3511 database with peer links recorded at 68-70

AFTER — actual captured migration command: vp run migrate-dev-db
$ node apps/server/scripts/migrate-dev-db.ts ⊘ cache disabled
Copying visible threads from /home/ubuntu/.t3/userdata/statev2.sqlite (read-only)...
Running migrations on the snapshot...
[03:54:09.435] INFO (#1): Migrations ran successfully {
  migrations: [ '68_ShellStopRequestIndex', '69_ThreadMessageSearch' ]
}
[03:54:09.436] WARN (#1): Database migration history diverges from this build; recorded migration ids are skipped, not reconciled by name. {
  divergent: [
    '70:PeerLinks (unknown to this build)',
    '71:PeerLinkFence (unknown to this build)',
    '72:WaitingLinkRequestIndex (unknown to this build)'
  ]
}
Pruning to 5 projects, 10 stopped threads each...
Compacting into /home/ubuntu/wt/issue-25289/.t3/userdata/statev2.sqlite...

Dev database ready: /home/ubuntu/wt/issue-25289/.t3/userdata/statev2.sqlite (91.8 MB)
  11533 orchestration events kept
  Migrations applied: 68_ShellStopRequestIndex, 69_ThreadMessageSearch

Aggregate pruning result from lead capture: 37 stopped threads retained; database 91.8 MB. Project labels omitted.

AFTER — actual captured startup command: vp run dev --no-seed
[03:54:27.137] INFO (#1): [dev-runner] mode=dev source=worktree /home/ubuntu/wt/issue-25289 serverPort=15602 webPort=7562 baseDir=/home/ubuntu/wt/issue-25289/.t3
[03:54:34.719] WARN (#48): Database migration history diverges from this build; recorded migration ids are skipped, not reconciled by name.
  divergent: [
    '70:PeerLinks (unknown to this build)',
    '71:PeerLinkFence (unknown to this build)',
    '72:WaitingLinkRequestIndex (unknown to this build)'
  ]
[03:54:36.125] INFO (#6516): Listening [startup address omitted]
[03:54:36.547] INFO (#6513): V2 orchestration recovery completed
  {
    terminalizedRuns: 0,
    stoppedSessions: 0,
    closedRequests: 0,
    retiredEffects: 0,
    requeuedEffects: 0
  }
Lead stopped the spawned dev runner via its captured session with Ctrl-C.
FRICTION: GET /api/health returned 404; this route does not exist. No health-200 claim is made. Readiness evidence is Listening at 03:54:36.125 and completed recovery at 03:54:36.547 with all five recovery counts zero.

CURRENT ISOLATED DATABASE — read-only verification during assembly
Python sqlite3.connect('file:/home/ubuntu/wt/issue-25289/.t3/userdata/statev2.sqlite?mode=ro', uri=True)
Only migration history and sqlite_master schema were queried; no thread/project contents were read for this evidence.
SQL: SELECT migration_id,name FROM effect_sql_migrations WHERE migration_id BETWEEN 68 AND 72 ORDER BY migration_id;
68 ShellStopRequestIndex
69 ThreadMessageSearch
70 PeerLinks
71 PeerLinkFence
72 WaitingLinkRequestIndex

SQL: SELECT type,name,sql FROM sqlite_master WHERE name IN ('orchestration_v2_projection_turn_items_stop_request_idx','orchestration_v2_projection_turn_items_waiting_link_idx','orchestration_v2_message_search') OR (type='trigger' AND name LIKE 'orchestration_v2_message_search_%') ORDER BY type,name;

index: orchestration_v2_projection_turn_items_stop_request_idx
CREATE INDEX orchestration_v2_projection_turn_items_stop_request_idx
    ON orchestration_v2_projection_turn_items(thread_id, run_id)
    WHERE type = 'run_interrupt_request'
  

index: orchestration_v2_projection_turn_items_waiting_link_idx
CREATE INDEX orchestration_v2_projection_turn_items_waiting_link_idx
    ON orchestration_v2_projection_turn_items(thread_id, updated_at DESC, turn_item_id DESC)
    WHERE type = 'link_request' AND status = 'waiting'
  

table: orchestration_v2_message_search
CREATE VIRTUAL TABLE orchestration_v2_message_search USING fts5(
      text,
      content = '',
      contentless_delete = 1,
      tokenize = 'trigram remove_diacritics 1'
    )

trigger: orchestration_v2_message_search_delete
CREATE TRIGGER orchestration_v2_message_search_delete
    AFTER DELETE ON orchestration_v2_projection_messages
    WHEN old.streaming = 0
    BEGIN
      DELETE FROM orchestration_v2_message_search WHERE rowid = old.rowid;
    END

trigger: orchestration_v2_message_search_insert
CREATE TRIGGER orchestration_v2_message_search_insert
    AFTER INSERT ON orchestration_v2_projection_messages
    WHEN 
  new.streaming = 0
  AND (
    new.role = 'assistant'
    OR (
      new.role = 'user'
      AND COALESCE(json_extract(new.payload_json, '$.createdBy'), 'user') = 'user'
    )
  )
  AND NOT EXISTS (
    SELECT 1 FROM orchestration_v2_projection_threads AS subagent_threads
    WHERE subagent_threads.thread_id = new.thread_id
      AND json_extract(subagent_threads.payload_json, '$.lineage.relationshipToParent') = 'subagent'
  )

    BEGIN
      INSERT INTO orchestration_v2_message_search (rowid, text)
      SELECT new.rowid, replace(replace(json_extract(new.payload_json, '$.text'), '’', ''''), '‘', '''')
      WHERE json_extract(new.payload_json, '$.text') IS NOT NULL;
    END

trigger: orchestration_v2_message_search_update
CREATE TRIGGER orchestration_v2_message_search_update
    AFTER UPDATE OF payload_json, streaming, role ON orchestration_v2_projection_messages
    WHEN (old.streaming = 0 OR new.streaming = 0)
      AND (
        old.streaming IS NOT new.streaming
        OR old.role IS NOT new.role
        OR json_extract(old.payload_json, '$.text') IS NOT json_extract(new.payload_json, '$.text')
        OR json_extract(old.payload_json, '$.createdBy')
          IS NOT json_extract(new.payload_json, '$.createdBy')
      )
    BEGIN
      DELETE FROM orchestration_v2_message_search WHERE rowid = old.rowid AND old.streaming = 0;
      INSERT INTO orchestration_v2_message_search (rowid, text)
      SELECT new.rowid, replace(replace(json_extract(new.payload_json, '$.text'), '’', ''''), '‘', '''')
      WHERE 
  new.streaming = 0
  AND (
    new.role = 'assistant'
    OR (
      new.role = 'user'
      AND COALESCE(json_extract(new.payload_json, '$.createdBy'), 'user') = 'user'
    )
  )
  AND NOT EXISTS (
    SELECT 1 FROM orchestration_v2_projection_threads AS subagent_threads
    WHERE subagent_threads.thread_id = new.thread_id
      AND json_extract(subagent_threads.payload_json, '$.lineage.relationshipToParent') = 'subagent'
  )

        AND json_extract(new.payload_json, '$.text') IS NOT NULL;
    END

LIMITATION: The recorded peer migrations 70 PeerLinks, 71 PeerLinkFence, and 72 WaitingLinkRequestIndex remain unknown to this build. Base/main has no peer migration implementations (git ls-tree checked); this evidence does not claim that main implements or fully validates their behavior. The fix preserves their existing schema/history while applying main migrations 68/69. The startup divergence warning is retained above.
Sanitization: startup pairing token/URL, project labels, secrets, thread/project contents, and database data are excluded. Only selected runtime lines, aggregate counts, migration names, and schema are included. Original logs and full database are not uploaded.