add codeline agent attribution for manual commits

[Soph]

This adds new fields to the metadata.json:

    "initial_attribution": {
      "calculated_at": "2026-01-23T14:30:00Z",
      "agent_lines": 142,
      "human_added": 12,
      "human_modified": 6,
      "human_removed": 3,
      "total_committed": 154,
      "agent_percentage": 92.2
    }

This is done by comparing the shadow branch against the commit that was made. Any change not in the shadow branch was made by the user. Based on that we calculate a percentage.

---

Note

Introduces commit-time attribution metrics and prompt-time tracking to quantify agent vs. human contributions in manual-commit flow.

• Adds initial_attribution to metadata.json with fields like agent_lines, human_added, human_modified, human_removed, total_committed, and agent_percentage; timestamps UTC
• Implements attribution calculation by diffing base → shadow (agent work) and shadow → head (post-checkpoint user edits), excluding binary files; retains attribution across multi-session merges
• Captures per-prompt user edits via new session state (PromptAttributions, PendingPromptAttribution) computed at prompt start from the worktree; stored on checkpoint save and cleared after condensation
• Extends manual-commit strategy to compute and persist attribution during condensation; logs debug info; converts session state to/from strategy types
• Adds comprehensive unit/integration tests (including deletion-only, no double-counting, staging vs worktree) and architecture docs; updates go.mod with go-diff dependency

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[Copilot]

Pull request overview

This PR adds line-level agent attribution tracking for manual commits by comparing the shadow branch (agent work) against HEAD (what was actually committed). The calculated metrics show how much of the committed code came from the agent unchanged versus human edits, including an agent percentage.

Changes:

• Adds InitialAttribution struct to capture line-level metrics (agent lines, human added/modified/removed, total committed, agent percentage)
• Implements diffing logic using github.com/sergi/go-diff/diffmatchpatch to compare checkpoint tree vs committed tree
• Integrates attribution calculation into the manual-commit condensation flow

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
cmd/entire/cli/checkpoint/checkpoint.go	Defines InitialAttribution struct and adds it to WriteCommittedOptions and CommittedMetadata
cmd/entire/cli/checkpoint/committed.go	Passes InitialAttribution through to metadata.json during checkpoint write
cmd/entire/cli/strategy/manual_commit_attribution.go	Implements CalculateAttribution with line-level diff logic, binary file handling, and edge case handling
cmd/entire/cli/strategy/manual_commit_attribution_test.go	Unit tests for diffLines, countLinesStr, and attribution calculation edge cases
cmd/entire/cli/strategy/manual_commit_condensation.go	Integrates attribution calculation into CondenseSession by comparing shadow tree to HEAD tree
cmd/entire/cli/strategy/manual_commit_test.go	Integration test verifying attribution is calculated and written to metadata.json

[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

[Copilot]

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 6 comments.

[Soph]

bugbot run

[Copilot]

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[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

[Copilot]

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

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Cursor Bugbot has reviewed your changes and found 3 potential issues.

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[Copilot]

Pull request overview

Copilot reviewed 15 out of 15 changed files in this pull request and generated 4 comments.