Store subagent transcripts as separate prompt records

[jwiegley]

Summary

• Parse Claude Code subagent transcripts from <session>/subagents/agent-<id>.jsonl into separate SubagentInfo structs instead of merging them into the parent transcript
• Add parent_id field to PromptRecord and PromptDbRecord to link subagent prompt records back to their parent
• Expand subagent metadata into separate prompt records at post-commit time and in virtual attributions, preserving thread hierarchy
• Make the v3→v4 DB migration idempotent: apply_migration() now catches "duplicate column name" errors from ALTER TABLE ADD COLUMN so a crash between the DDL and the version-bump doesn't brick the database on restart

Closes #371

Design

Subagent transcripts stored in Claude Code's subagents/ directory are now collected as SubagentInfo structs during JSONL parsing rather than being flattened into the parent transcript. These are propagated through the checkpoint pipeline via PromptUpdateResult::Updated and stored as JSON metadata (__subagents key) on the parent checkpoint.

At post-commit time (and in virtual attributions), the subagent metadata is expanded into separate PromptDbRecord entries, each with a unique hash ID and a parent_id linking back to the parent prompt. This preserves the natural thread structure of agentic coding sessions.

DB schema migrated from version 3 to 4 to add the parent_id TEXT column to the prompts table. The migration is idempotent — if the column already exists (e.g. from a previous partial migration), the error is caught and silently skipped.

Updates since last revision

• Merged latest main into the branch and resolved merge conflicts in tests/claude_code.rs (added new subagent test names to the reuse_tests_in_worktree! macro)
• Made apply_migration() idempotent by catching "duplicate column name" SQLite errors instead of crashing
• Added test_initialize_schema_handles_preexisting_parent_id_column to verify the idempotency path
• Fixed missing parent_id: None in tests/worktrees.rs PromptRecord initializer (compilation error)
• Fixed formatting (extra blank line in tests/claude_code.rs)

Test plan

• cargo clippy — no warnings
• cargo test --test claude_code — all 24 tests pass
• cargo test --test agent_presets_comprehensive — all 58 tests pass
• New test: test_parse_claude_code_jsonl_with_subagents verifies subagents are returned separately
• Updated test: test_parse_claude_code_jsonl_without_subagents_dir verifies empty vec for no subagents
• New test: test_initialize_schema_handles_preexisting_parent_id_column verifies idempotent migration
• New test fixtures: claude-code-with-subagents.jsonl and subagents/agent-test-sub-1.jsonl
• CI: Format ✅, Lint (all platforms) ✅, Ubuntu tests (hooks/wrapper/both) ✅

Review & Testing Checklist for Human

There are 4 items to verify given the scope of DB schema + query changes:

• Idempotency approach: Verify that catching "duplicate column name" via string matching is acceptable for SQLite migrations (this is a common pattern but relies on error message text)
• SQL query coverage: Spot-check that all SELECT, INSERT, and UPDATE queries in internal_db.rs include the new parent_id column in the correct position (column order matters for positional binding)
• Test coverage: Confirm all PromptRecord initializers in test files include parent_id: None (compilation would fail if any were missed, but worth double-checking)
• Subagent parsing correctness: Review test_parse_claude_code_jsonl_with_subagents to ensure subagent messages are correctly separated from the parent transcript and not duplicated

Notes

• The parent_id field is Option<String> with #[serde(default)], so existing serialized data without this field will deserialize correctly
• The migration is safe to run multiple times — if the column already exists, the error is caught and the version is still updated
• All Ubuntu CI checks are passing; macOS and Windows checks are still pending but not blocking per user request

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Requested by: @svarlamov

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[svarlamov]

Append subagent messages to the main transcript in sorted filename order for deterministic results

I'm not a huge fan of this Claude... May have mentioned it elsewhere, but can we add them as normal prompts into the authorship log but just include a parentId that will point to the parent prompt?

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✅ jwiegley
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