Checkpoints v2: write compact transcript file + metadata

[computermode]

Writes the transcript.jsonl file to refs/entire/checkpoints/v2/main when the v2 checkpoints setting is enabled.

Tested locally:

➜  test-repo git:(test-v2-checkpoints) ✗ git show-ref refs/entire/checkpoints/v2/main
d4cea66ced1e346fa584113e982d16fc7c1a50d8 refs/entire/checkpoints/v2/main

➜  test-repo git:(test-v2-checkpoints) ✗ git show refs/entire/checkpoints/v2/main:3c/ed2b94d513/0/transcript.jsonl

{"v":1,"agent":"claude-code","cli_version":"v0.5.2-dev-717d7810c","type":"user","ts":"2026-04-01T20:52:39.072Z","content":[{"id":"c5e73887-be32-4c29-9461-ead695f305da","text":"update v2 to add \"testing again\""}]}
{"v":1,"agent":"claude-code","cli_version":"v0.5.2-dev-717d7810c","type":"assistant","ts":"2026-04-01T20:52:43.270Z","id":"msg_01BXKpfEoL22fQmiskWPSjbe","input_tokens":3,"output_tokens":123,"content":[{"id":"toolu_01USUsrAM8y5vt4i3z9qVhAj","input":{"pattern":"v2|test v2","output_mode":"files_with_matches"},"name":"Grep","result":{"output":"Found 2 files\ntest-v2.md\n.entire/settings.json","status":"success","matchCount":2},"type":"tool_use"}]}
{"v":1,"agent":"claude-code","cli_version":"v0.5.2-dev-717d7810c","type":"assistant","ts":"2026-04-01T20:52:47.454Z","id":"msg_0185d7DbCwbZYnYnVrMaWsXU","input_tokens":1,"output_tokens":75,"content":[{"id":"toolu_01J1do5pvCSyd327EtebzwkC","input":{"file_path":"/Users/ninawork/entire/test-repos/test-repo/test-v2.md"},"name":"Read","result":{"output":"1\ttesting v2\n2\t","status":"success","file":{"filePath":"/Users/ninawork/entire/test-repos/test-repo/test-v2.md","numLines":2}},"type":"tool_use"}]}
{"v":1,"agent":"claude-code","cli_version":"v0.5.2-dev-717d7810c","type":"assistant","ts":"2026-04-01T20:52:50.594Z","id":"msg_01J2S6HmZXNVFpcgYKzZJrKX","input_tokens":1,"output_tokens":120,"content":[{"id":"toolu_01AWD7CRQH1EACsSy91T8Swy","input":{"replace_all":false,"file_path":"/Users/ninawork/entire/test-repos/test-repo/test-v2.md","old_string":"testing v2","new_string":"testing v2\ntesting again"},"name":"Edit","result":{"output":"The file /Users/ninawork/entire/test-repos/test-repo/test-v2.md has been updated successfully.","status":"success","file":{"filePath":"/Users/ninawork/entire/test-repos/test-repo/test-v2.md"}},"type":"tool_use"}]}
{"v":1,"agent":"claude-code","cli_version":"v0.5.2-dev-717d7810c","type":"assistant","ts":"2026-04-01T20:52:54.560Z","id":"msg_015Nd5ycH2fJCAjQLJiaG9iL","input_tokens":1,"output_tokens":23,"content":[{"text":"Done. Added \"testing again\" on a new line in `test-v2.md`.","type":"text"}]}

➜  test-repo git:(test-v2-checkpoints) ✗ git ls-tree -r refs/entire/checkpoints/v2/main

100644 blob 6560fea9b1fd7f2b6a0c7114f2b7150a4b14f221	3c/ed2b94d513/0/metadata.json
100644 blob 5f52afef5f351f5f47a3ae1c9d96a099de5d6cba	3c/ed2b94d513/0/prompt.txt
100644 blob eb88d390b34ee8f7de5ce494f2e88dc322aa2f29	3c/ed2b94d513/0/transcript.jsonl
100644 blob 14587f39e987cb315b26e8ecd475d16186d826be	3c/ed2b94d513/0/transcript_hash.txt
100644 blob da48506b27531e8fe67eb24f426f1042fd277481	3c/ed2b94d513/1/metadata.json
100644 blob 54bd80c02ecc778a79652855ec2c26e5f1341cc5	3c/ed2b94d513/1/prompt.txt
100644 blob f9f36ff2d2a78f79ad154268f626d67d8ce0645d	3c/ed2b94d513/1/transcript.jsonl
100644 blob a3c68608f5db097698aef90cbd53562ad53074f0	3c/ed2b94d513/1/transcript_hash.txt
100644 blob 93f1890701bab01ed41554ae068ec07999563877	3c/ed2b94d513/metadata.json

---

Note

Medium Risk
Changes v2 checkpoint persistence semantics by adding new artifacts (transcript.jsonl + hash) to the permanent /main ref and updating stop-time finalization to rewrite them, which could affect consumers that read v2 metadata paths or expect transcripts only under /full/current. Logic is guarded by the v2 setting and includes redaction/skip-on-error behavior, but it touches core checkpoint storage/update flows.

Overview
Adds support for writing a compact, redacted transcript artifact to v2 checkpoints: transcript.jsonl plus transcript_hash.txt are now stored on refs/entire/checkpoints/v2/main alongside metadata/prompts, while raw full.jsonl remains on refs/entire/checkpoints/v2/full/current.

Extends checkpoint write/update options with CompactTranscript, updates v2 /main write + UpdateCommitted to create/replace these blobs and keep root metadata.json session paths in sync (with transcript/content_hash now optional). Manual-commit condensation and stop-time finalization now generate the compact format (with secret redaction) when v2 is enabled, and tests/integration assertions are updated to validate the new files and redaction behavior.

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[Copilot]

Pull request overview

Adds support for writing a compact transcript.jsonl (Entire Transcript Format) and its hash to the v2 checkpoints /main ref during dual-write, so /main can carry lightweight transcript data while /full/current continues to store the raw transcript.

Changes:

• Generate and attach a compact transcript during condensation and stop-time finalization when v2 checkpoints are enabled.
• Persist transcript.jsonl + transcript_hash.txt to v2 /main, and expose their paths in SessionFilePaths.
• Extend unit/integration tests to validate the compact transcript artifacts on v2 refs.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/manual_commit_hooks.go	Generates compact transcript during stop-time finalization for v2 /main.
cmd/entire/cli/strategy/manual_commit_condensation.go	Adds compact transcript generation helper and wires it into condensation writes.
cmd/entire/cli/paths/paths.go	Introduces constants for compact transcript filename + hash filename.
cmd/entire/cli/integration_test/v2_dual_write_test.go	Verifies compact transcript + hash exist on v2 /main in integration flows.
cmd/entire/cli/checkpoint/v2_store_test.go	Adds unit tests for writing/updating compact transcript and hash on v2 /main.
cmd/entire/cli/checkpoint/v2_committed.go	Implements writing compact transcript + hash on /main and updates related comments.
cmd/entire/cli/checkpoint/checkpoint.go	Extends checkpoint option structs and SessionFilePaths to include compact transcript paths.

[computermode]

bugbot review

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