[Bug]: Claude Code prompts not saved

[MattiaSilvestri]

What broke?

git ai blame --json correctly attributes lines to the Claude Code session/turn that wrote them, and the resulting prompts object is populated with agent_id, human_author, other_files, and commits. However:

• total_additions, total_deletions, accepted_lines, and overriden_lines are always 0, even for a prompt that produced 60+ attributed lines.
• git ai show-prompt <prompt_id> --commit <sha> returns the same prompt object but with no messages field at all — despite prompt_storage being explicitly set to "notes" before the commit was made.

This looks related to #1475 (closed) — same general area (prompt/transcript content not persisting into the git note), but a different manifestation: instead of an empty prompts: {}, the prompt record exists and is correctly linked to the right lines/commit, just missing the content-bearing fields. Also, mine is Claude Code specifically, not Codex/Copilot, and the prompt IDs are in the session::turn composite format rather than the flat hex ID shown in the docs' own example output.

Steps to reproduce

1. Install/update git-ai to latest, confirm with git-ai --version → 1.7.0
2. git ai config set prompt_storage notes
3. Start a Claude Code session in a repo, ask it to edit a file (e.g. multi-line edit across ~60 lines)
4. Commit the change
5. Run git ai blame <file> --json → lines are correctly attributed to the new session/turn
6. Run git ai show-prompt "<prompt_id>" --commit <commit_sha> on that prompt ID

Expected vs actual behavior

Expected: show-prompt returns a populated messages array with the actual prompt/response transcript, and the prompts object in blame --json reflects real total_additions/accepted_lines matching the attributed line count.

Actual:

blame --json output (I asked claude to anonymize the data):

{
  "lines": {
    "44-104": "s_aaaaaaaaaaaaaa::t_bbbbbbbbbbbbbb"
  },
  "prompts": {
    "s_aaaaaaaaaaaaaa::t_bbbbbbbbbbbbbb": {
      "agent_id": { "tool": "claude", "id": "00000000-0000-0000-0000-000000000000", "model": "claude-opus-5" },
      "human_author": "Test User <test.user@example.com>",
      "total_additions": 0,
      "total_deletions": 0,
      "accepted_lines": 0,
      "overriden_lines": 0,
      "other_files": [],
      "commits": ["0000000000000000000000000000000000000a"]
    }
  }
}

show-prompt output for the same commit/prompt ID:

{
  "commit": "0000000000000000000000000000000000000a",
  "prompt": {
    "accepted_lines": 0,
    "agent_id": { "id": "00000000-0000-0000-0000-000000000000", "model": "claude-opus-5", "tool": "claude" },
    "human_author": "Test User <test.user@example.com>",
    "overriden_lines": 0,
    "total_additions": 0,
    "total_deletions": 0
  },
  "prompt_id": "s_aaaaaaaaaaaaaa::t_bbbbbbbbbbbbbb"
}

No messages field present at all.

Diagnostics (git-ai debug)

runtime_config:
    {
      "git_path": "/usr/bin/git",
      "exclude_prompts_in_repositories": [],
      "include_prompts_in_repositories": [],
      "allow_repositories": [],
      "exclude_repositories": [],
      "telemetry_oss_disabled": false,
      "telemetry_enterprise_dsn": null,
      "disable_version_checks": false,
      "disable_auto_updates": false,
      "update_channel": "latest",
      "feature_flags": {
        "lite_mode": false,
        "auth_keyring": false,
        "transcript_streaming": true,
        "transcript_sweep": true,
        "checkpoint_debug_log": false,
        "bash_checkpoints_v2": false,
        "daemon_log_upload": true,
        "rewrite_metrics_events": false,
        "token_usage_metrics": false
      },
      "api_base_url": "https://usegitai.com",
      "prompt_storage": "notes",
      "default_prompt_storage": null,
      "api_key": null,
      "quiet": false,
      "allow_superuser": false,
      "author": {},
      "custom_attributes": {},
      "git_ai_hooks": {},
      "codex_hooks_format": "config_toml",
      "notes_backend": {
        "kind": "git_notes",
        "backend_url": "https://usegitai.com"
      },
      "transcript_streaming_lookback_days": 7,
      "max_checkpoint_file_size_bytes": 3145728,
      "max_checkpoint_total_size_bytes": 33554432,
      "max_checkpoint_total_lines": 500000,
      "daemon_memory_limit_mb": null
    }

== Git AI Login ==
Credential backend: file
Status: logged out

== Git Environment ==
No GIT_AI_*, GITAI_*, or GIT_* environment variables are set.

Extra context (optional)

• prompt_storage was confirmed set to "notes" (not "default") before the commit in question was made, so this isn't the "changed setting doesn't retroactively backfill old commits" case.
• notes_backend.kind is "git_notes" (local), not "http".
• Tested on a fresh commit specifically to rule out the config-not-applied-yet explanation.