Bug

Turn diffs ("Loading checkpoint diff…" / "Filesystem checkpoint is unavailable for turn N") never resolve after a Codex turn completes, even when the project is a valid git repository.

Root cause

There is a race between two independent event handlers that both react to turn completion:

1. ProviderRuntimeIngestion handles turn.diff.updated events and immediately dispatches thread.turn.diff.complete with a placeholder checkpoint entry:

   • checkpointRef: "provider-diff:<eventId>" (not a real git ref)
   • status: "missing"
   • files: []

   (apps/server/src/orchestration/Layers/ProviderRuntimeIngestion.ts, lines 1064-1083)

2. CheckpointReactor handles turn.completed events and is supposed to capture a real git-ref-based checkpoint via CheckpointStore.captureCheckpoint, then dispatch thread.turn.diff.complete with the actual diff data.

   (apps/server/src/orchestration/Layers/CheckpointReactor.ts, lines 150-298)

The problem: ProviderRuntimeIngestion wins the race and inserts the placeholder into thread.checkpoints first. When CheckpointReactor later processes turn.completed, it checks:

if (thread.checkpoints.some((checkpoint) => checkpoint.turnId === turnId)) {
  return; // ← early exit, real capture never happens
}

(line 169)

Since the placeholder already has the same turnId, the real git checkpoint is never captured. The DiffPanel then tries to resolve provider-diff:UUID via git rev-parse, which fails because it's not an actual git ref.

Observed behavior

• Server logs show thread.turn-diff-completed events with checkpointRef: "provider-diff:..." and status: "missing"
• DiffPanel shows "Loading checkpoint diff..." indefinitely, then "Filesystem checkpoint is unavailable for turn N"
• No refs/t3/checkpoints/ git refs are created for the affected turns

Reproduction

1. Add any git-initialized project
2. Send a message that triggers file changes (e.g., "add a comment to README")
3. Wait for turn to complete
4. Open the diff panel → stuck on "Loading checkpoint diff..."

Suggested fix

The dedup check in CheckpointReactor (line 169) should either:

• Only skip if an existing checkpoint has a non-placeholder status (i.e., skip "missing" entries), or
• Replace/upgrade placeholder checkpoints with the real git-based checkpoint when one becomes available

Additionally, there is a secondary CWD inconsistency worth noting: CheckpointReactor turn-completion capture prefers sessionRuntime.cwd while CheckpointDiffQuery only uses resolveThreadWorkspaceCwd. If these ever diverge, refs would be written to one repo but looked up in another.

Environment

• T3 Code dev (main branch)
• Codex provider with GPT-5.4
• Linux (Arch)