feat(state): add parent_entry_id on the message table for fork support

[hongqitai]

Summary

Refs #2082 add fork support to state crate, add parent_entry_id to message table and current_leaf_id to threads table

Change

• change some structs and other crate to add fields to match the database
• init_schema: use user_version to determine whether an update is needed, on update do old migration first then add new column and use created_at to make chain
• append_message: add message under current leaf message and set current to new
• list_messages: list the parent chain of current leaf
• (Add) list_leaf_messages: return messages on leaf node of the message tree
• (Add) fork_at_message: add message under specified message and set current to new
• (Test) init_schema_migration: make sure it can migration from existing sessions
• (Test) test_fork: test forks a 5-message session and proves both leaves are queryable independently

Testing

• [ x ] cargo fmt --all -- --check
• [ x ] cargo clippy --workspace --all-targets --all-features
• [ x ] cargo test --workspace --all-features

Checklist

• [ x ] Updated docs or comments as needed
• [ x ] Added or updated tests where relevant
• [ x ] Verified TUI behavior manually if UI changes

Greptile Summary

This PR adds fork support to the state crate by introducing parent_entry_id on the messages table and current_leaf_id on the threads table, enabling a message-tree structure where conversations can branch from any historical message.

• init_schema is now versioned via PRAGMA user_version: on first open it runs CREATE TABLE IF NOT EXISTS for all tables and immediately ALTER TABLE to add the two new columns, sets user_version = 1, and wraps everything in a BEGIN/COMMIT to make the migration atomic.
• append_message is rewritten as a transaction that reads current_leaf_id, inserts the new message with that value as parent_entry_id, then advances current_leaf_id; list_messages switches from a flat ORDER BY created_at to a recursive CTE that walks the parent chain from current_leaf_id.
• New public API: fork_at_message inserts a child under an arbitrary existing message and sets it as the new current leaf; list_leaf_messages returns all tip nodes; set_current_leaf_id lets callers switch the active branch.

Confidence Score: 3/5

The migration parent-chain reconstruction uses strict less-than on a seconds-precision timestamp, which silently truncates conversation history for any existing thread where two or more messages share the same second.

Any thread with rapid message exchanges — the common case for LLM tool-call/response cycles — will have messages with identical created_at values. The migration sets parent_entry_id to NULL for all of them, breaking the ancestor chain. list_messages then returns only the fragment from current_leaf_id to the first orphan, dropping older messages permanently and irreversibly.

crates/state/src/lib.rs — the UPDATE messages SET parent_entry_id subquery in the migration block (lines 243–250).

Important Files Changed

Filename	Overview
crates/state/src/lib.rs	Core state layer rewritten to support fork: adds parent_entry_id/current_leaf_id, new CTE-based list_messages, fork_at_message, list_leaf_messages, set_current_leaf_id. Migration timestamp collision (strict < on created_at) can break the parent chain for existing sessions with same-second messages.
crates/core/src/lib.rs	Adds current_leaf_id: None to the ThreadMetadata literal in persist_thread; upsert_thread's ON CONFLICT clause intentionally omits current_leaf_id so the stored value is preserved.
crates/state/tests/parity_state.rs	Adds two new tests: init_schema_migration (migration from a pre-existing schema) and test_fork (full fork/leaf/clear lifecycle). A stray dbg! macro is left in test_fork.

Comments Outside Diff (1)

1. crates/core/src/lib.rs, line 624-647 (link)

   persist_thread hard-codes current_leaf_id: None, wiping it on every resume

   persist_thread builds a ThreadMetadata literal with current_leaf_id: None. Because upsert_thread's ON CONFLICT clause includes current_leaf_id = excluded.current_leaf_id, any call to persist_thread on an existing thread writes NULL over the value that append_message painstakingly maintained. resume_thread_with_history calls persist_thread before it conditionally appends history (line 502), so resuming a thread that has no new history clears current_leaf_id permanently — after which list_messages returns an empty list because the CTE base case WHERE id = NULL never matches.

   

_{Reviews (5): Last reviewed commit: "fix: upsert_thread will not set current_..." | Re-trigger Greptile}

[gemini-code-assist]

Code Review

This pull request introduces message branching and forking capabilities to the state store by adding current_leaf_id to threads and parent_entry_id to messages, alongside database schema migrations and recursive CTE queries. The code reviewer identified a critical bug where the recursive CTE query returns messages in reverse chronological order, and suggested handling limit == 0 early. Additionally, the reviewer pointed out that using created_at in migrations can cause issues due to duplicate timestamps and recommended using the auto-incrementing id instead. Other feedback includes simplifying an Option<String> type to String and updating test assertions to match chronological ordering.

[greptile-apps]

set_current_leaf_id accepts current_leaf_id as &str even though the underlying column is INTEGER and every other call-site works with i64. SQLite silently coerces the string, but callers are forced to call .to_string() on an integer they already hold, which is type-unsafe. The parameter should be i64.

Suggested change

	pub fn set_current_leaf_id(&self, thread_id: &str, current_leaf_id: &str) -> Result<()> {
	pub fn set_current_leaf_id(&self, thread_id: &str, current_leaf_id: i64) -> Result<()> {

Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!

[hongqitai]

fix all problem without coding style, because of I find other code in this crate use "&str" to take int value