Fix a bug that caused session conflicts

[Soph]

This was reported by @dipree but also @georg might have seen variations of it. After digging through the entire/sessions logs and what data we had (and trying different theories) this is where we landed:

  The Bug Scenario

  1. Session A (914e68cc) starts
    - InitializeSession creates state with CheckpointCount: 0
  2. User runs a Task (subagent) in Session A
    - PreToolUse[Task] fires → createStartingAgentCheckpoint → SaveTaskCheckpoint
    - This creates a commit on the shadow branch (even with no file changes!)
    - CheckpointCount stays at 0
  3. User closes Claude without main agent making file changes
    - Stop hook fires but commitWithMetadata returns early ("No files were modified")
    - Session A state: CheckpointCount: 0, shadow branch has commits
  4. Session B (f9b37e51) tries to start
    - InitializeSession checks: state == nil || state.CheckpointCount == 0 → TRUE
    - Sees shadow branch with commits tagged 914e68cc
    - Loads Session A's state file (exists with CheckpointCount: 0)
    - Returns SessionIDConflictError
  5. User sees the error message about "orphaning existing work"
    - But working tree is clean (task changes were undone, committed, or never existed)

This is probably the important aspect:

• This creates a commit on the shadow branch (even with no file changes!)

Since that commit caused then the other session to fail to start since there was a commit in the shadow branch but no local changes, so it gave the wrong instructions.

---

Note

Eliminates creation of "starting" subagent checkpoints and empty marker commits to prevent session conflicts and reduce noise.

• PreToolUse[Task]: now only captures pre-task state; no checkpoint/commit is created
• AutoCommitStrategy.commitTaskCodeToActive: skips commit when no file changes; removes TaskStart handling
• Removes IncrementalTypeTaskStart, FormatSubagentStartMessage, and related tests; simplifies FormatIncrementalSubject
• Updates integration/unit tests to expect a single completed checkpoint (no start checkpoint)
• Docs updated to reflect new hook behavior and when checkpoints are created

^{Written by Cursor Bugbot for commit 49bda72. This will update automatically on new commits. Configure here.}

[Copilot]

Pull request overview

This PR fixes a session conflict bug where a new session would fail to start after a previous session ran a Task (subagent) that made no file changes. The bug occurred because the PreTask hook created a shadow branch commit even with no file changes, but didn't increment the session's CheckpointCount. This caused the session initialization logic to incorrectly detect a conflict.

Changes:

• Removed createStartingAgentCheckpoint() function that created empty "starting agent" commits during PreTask hooks
• Updated PreTask hook to only capture local state (for computing new files later) without creating shadow branch commits
• Added clarifying comment that commits are only created when tasks actually result in file changes

[Copilot]

Pull request overview

Copilot reviewed 7 out of 7 changed files in this pull request and generated no new comments.

[khaong]

Looks good - just updated some of the docs to align.