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Dotta 73eee2c0d6 docs: Pi core production readiness evidence (5/5) (#14956) 
## Thinking Path

> - Paperclip manages AI agents and their work.
> - The experimental Runner owns provider processes and durable
sessions.
> - Pi needs working task execution and human controls.
> - The five-PR stack must preserve changes already on master.
> - The runtime implementation has merged in #14921; this layer carries
the next documentation changes.
> - This PR belongs to native GitHub stack #15602, ending at #14956.

## Linked Issues or Issue Description

Refs #14436, #14631, #14743 and #14956.

Ship Pi 1.0 through the experimental Paperclip Runner. The five PRs are
#14921, #14922, #14923, #14924 and #14956. The user authorized the
complete merge after checks pass. Existing `pi_local` execution is
unchanged. Accounting and wider provider/platform qualification remain
deferred.

## What Changed

- Record the seven source-bound Pi core passes and retained
failed-attempt provenance.
- Document agent-file artifacts, warm instruction-root recovery, final
task replies, and installed Runner verification.

## Verification

- Full local `pnpm -r typecheck` passes, including Runner Rust, server
and UI. Focused integration checks pass: 194 Runner
admission/environment tests, 63 profile/credential tests with one
expected skip, 152 Dot/UI configuration tests, and Pi transcript/notice
tests.
- Full local `pnpm build` passes on the final source.
- Fresh final-source checks pass: all 698 Rust workspace tests (32
binaries), 156 credential/profile/controller tests with one expected
skip, Runner TypeScript typecheck, and 20 package/setup/sandbox tests.
- The profile-21 Pi materializer passes on the native host with the
official pinned Node 24.21.0 and its npm. It verifies all 150 locked
packages, the patched dependency and the exact closure. Setup/package
bundle tests and UI token gates pass.
- The old hashes were reproduced for all three supported targets before
calculating the patched graph. New closure hashes are darwin-arm64
`282022db10150c6632b3444df421342e7d534bdf5d5fb1097a2e79d0625a2bcf`,
darwin-x64
`64e251e19009f755c0b04f73ce2138246faab71a961b0f13d75ebfcc34bef12e`, and
linux-x64
`713b1fdff42fb56a1518bdc084f181d70bee8ebadc3e4b1d76321ed9108c8410`.
Independent native platform execution is separate from graph identity
reproduction.
- Historical cloud qualification remains unchanged: all seven core cases
pass on shipping source `10dc43c9ec65d88c2f782d62afb296d09494f215`,
harness `1a4408a48cfb5a1f094a311141c257c92cd7a893`, image
`sha256:5b3a775b383591bda1b0c1889e509acc70ce7f37c53f09733c81d59037f02280`,
and accepted Sonnet 4.6/low fixture. All 215 canonical files and all
seven cleanup checks pass independent verification. These are profile-19
results and are not relabeled as fresh profile-22 runs.
- Current Pi digest:
`sha256:e92078bee3c23bec4100aa589013a44613d054cd686826534025d8019e9f39a9`.
[The readiness
plan](https://github.com/paperclipai/paperclip/blob/codex/pi-production-readiness/doc/plans/2026-10-02-pi-production-readiness.md)
preserves campaign and failed-attempt provenance.
- Merge only after every PR's current-head CI and fresh review pass.
Linux CI covers the full suites, build and browser tests. The local
embedded Postgres API-authority suite cannot start on this macOS/Node 26
host, so Linux CI must confirm that suite.

### Fresh profile-22 core qualification — 2026-10-08

All seven accepted core cases pass canonically on Pi profile 22, with
`openrouter/anthropic/claude-sonnet-4.6` and native-confirmed low
thinking. This model is a fixture; production accepts the caller's
explicit Pi provider/model.

Runtime/install source: `3241a992f2a7703e59e97ed0fd3e5d6405de4401`.
Frozen accepted harness: `1a4408a48cfb5a1f094a311141c257c92cd7a893`.
Immutable cloud image:
`ghcr.io/paperclipai/paperclip-daytona-runner@sha256:506f22db7edd78f37c0c40bec1cc084af1850455026dbf467194bfbb8fcef141`.
Pi digest:
`sha256:e92078bee3c23bec4100aa589013a44613d054cd686826534025d8019e9f39a9`.

[Hosted Linux image and clean-install
verification](https://github.com/paperclipai/paperclip/actions/runs/37868328023)
passes, including all 20 source-bound archives, normal CLI/Pi setup,
companion import and the production pack reader. This exact installation
source includes the latest master integration and the corrected Pi warm
instruction-root fence. Full local typecheck/build and current-head
hosted CI verify the final stack. All 13 focused real-root regressions
pass. The full local executor suite passed 662 tests; 15 database tests
could not start the Mac embedded PostgreSQL service. Hosted Linux CI
passes the full required verification and E2E checks. These fresh
results keep their own source identity; profile-19 results remain
historical.

| Core path | Canonical campaign | Retained archive SHA-256 |
| --- | --- | --- |
| File edit, validation, download and Done |
`pi-core22-replyfix-0-1791511228` | 23 files;
`a473e8603a3dd4737863291f8d3d1e392391f0b16d433c3e0e0e9d8baf7a97b0` |
| Pending question and controller restart |
`pi-core22-replyfix-1-1791511376` | 33 files;
`6b829c4eb74e1f32a89c692a4ae7130dbfc1c6d3cf13915effe2103d9e242c8e` |
| Three-turn session/process/workspace continuity |
`pi-core22-replyfix-2-1791511587` | 23 files;
`7a87021f8f9a3fdd3c58bb4467f8d82c635e3ea4795d6e75f144d9aa14818df8` |
| Four typed questions and browser reconnects |
`pi-core22-replyfix-3-1791511881` | 42 files;
`9e31755252be1f4f9cb0626c984c142d4d1ae5f5bee3a7af08444db8d12c280a` |
| Plan approval and completion | `pi-core22-replyfix-4-1791512031` | 22
files;
`a0383ce1aab38e7b5a25ce0e9dd3bebea5c037ebd96ae6b29dae19015da2ae2c` |
| Same-turn steering and permission denial |
`pi-core22-replyfix-5-1791512261` | 39 files;
`c929b8c7070f0b66aedc17e65ca46e6beab1e363926ac9f7e2a75fb250f05949` |
| Stop during pending permission | `pi-core22-replyfix-6-1791512390` |
33 files;
`7f0a58ae0f4d5bfc76149435f4e322537089c5bd16e7ffe9b5ad71f10a621a07` |

All 215 canonical files (28714587 bytes) are independently
hash-verified. All seven cleanup grades pass, with no owned runtime
process or temporary root after each case. Automatic retries are zero.
The owned cloud host stopped normally after retention. The prior
profile-22 warm attempt remains failed and separately retained: archive
SHA-256
`1e54eba5ec72b50cee1534b23d1d1d4f21a090006b8a64501ba70db972abfde5`. Its
original canonical classification is preserved. Diagnosis reproduced a
product bug comparing an agent-files root against an unset
checkpoint-only field. The fix stores the admitted physical root
separately from the adopted per-run collection capability. The real-root
regression fails before the fix and passes afterward, including
rejection of a changed physical root. Fixture, grader, model and all
seven accepted case IDs are unchanged; this fresh campaign tests
final-reply publication after file registration first. The intermediate
restart attempt also remains failed and retained: archive SHA-256
`5dcaefdf1d17cf4cd54fd4cf810f45e736667392339b8ce7caf08bb4e225277f`. Its
original canonical classification is preserved. Pi resumed, wrote the
verified answer and completed its task; exact runner suspension was
proven, but idle stop consumed about 5.2s and left under 3s for the
drain acknowledgement. The Pi-only default shutdown grace is now 15s,
preserving a full 5s drain round trip and a finite suspension reserve.
Explicit caller deadlines, other provider defaults, literal drain
receipts and exact suspension identity checks remain unchanged. The
timing regression fails before this correction and passes afterward; all
18 focused settlement tests and Runner typecheck pass. The final-source
file attempt is also preserved as failed (`candidate_failure`), archive
SHA-256
`db6767b6773ea618997927ac77bdb005a5ac81492c7b9c0ffbc900449f829bc9`.
Native edit, validation, exact downloadable artifact and Done/succeeded
all passed, and the exact final reply was durably recorded. A workspace
recovery owner completed before the live heartbeat reached presentation,
leaving that reply absent from task chat. Recovery now materializes only
a completed final reply from the accepted turn of an ordinary internal
Done task, preserving issue/run/contract binding, suppression,
external-chat authorization and same-run deduplication. The database
regression covers the generated file-preparation receipt, suppression,
unapproved external continuation and replay. Server typecheck and all 49
response-selection tests pass; hosted Linux verifies the database
regression because embedded PostgreSQL cannot start on this Mac.

The delayed-final-answer database regression passes on [the final
root-source Linux server
shard](https://github.com/paperclipai/paperclip/actions/runs/37868262553/job/113628594152),
alongside 1,108 passing tests. The first root Runner shard had one
unchanged durable-resume test exceed its 5-second timeout; the identical
top-source shard and the isolated exact test passed. One rerun of that
failed job and its required aggregate passed without source or test
changes. The original failed job log and the single-rerun receipt remain
retained.

### October 9 merge verification

Current merge head: `e77273aa0fce5991a5b5dd193734fd6b0a6542d3`. All
current-head checks pass, including `ci / verify` and `ci / e2e`;
exact-head Greptile review is 5/5 with no unresolved threads. Current
master conflicts are resolved. The user authorized the maintainer
override of the code-owner review gate after these checks. The seven
retained live core cases remain bound to source
`3241a992f2a7703e59e97ed0fd3e5d6405de4401` and its recorded cloud image.

## Risks

- The security correction changes the dependency closure and profile
identity. Old sessions must reopen on the new profile. Exact identities
and credential bindings fail closed.
- The runner remains experimental and requires explicit selection.
Legacy Pi Local is unchanged. Caller model IDs pass through; the E2E
model is a fixture.
- Accounting and the broad platform/provider matrix remain deferred.
This merge does not publish a release or deploy a service.

## Model Used

OpenAI GPT-6 through Codex assisted with reasoning, repository
inspection, editing and tool use. The exact serving ID and context
window are not exposed in this session. Final live qualification uses Pi
1.0.0 with `openrouter/anthropic/claude-sonnet-4.6` and native-confirmed
low thinking.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge
 2026-10-09 11:15:09 -05:00
DottaandPaperclip 57e977be72 feat: integrate Pi 1.0 into the experimental Runner (#14921) 
## Thinking Path

> - Paperclip manages AI agents and their work.
> - The experimental Runner owns provider processes and durable
sessions.
> - Pi needs working task execution and human controls.
> - The five-PR stack must preserve changes already on master.
> - Each layer now carries the complete integrated source for a safe
sequential fallback.
> - This PR belongs to native GitHub stack #15602, ending at #14956.

## Linked Issues or Issue Description

Refs #14436, #14631, #14743 and #14956.

Ship Pi 1.0 through the experimental Paperclip Runner. The five PRs are
#14921, #14922, #14923, #14924 and #14956. The user authorized the
complete merge after checks pass. Existing `pi_local` execution is
unchanged. Accounting and wider provider/platform qualification remain
deferred.

## What Changed

- Recover missing final replies after workspace finalization changes
owners, using accepted-turn evidence without rerunning work or granting
external-chat publication.
- Preserve the admitted Pi instruction root across warm runs, while
retaining changed-root rejection.
- Give Pi a bounded 15-second default shutdown grace so stop, drain
acknowledgement and durable suspension can complete. Explicit deadlines
and other providers retain their existing behavior.
- Integrate the Pi 1.0 runtime and master contracts.
- Use Pi profile 22. Preserve explicit caller-selected models and exact
native thinking levels. Keep Pi's wrapper, helper, extension and
question/control behavior unchanged from the qualified profile-19
runtime.
- Preserve master's Dot lifecycle and consent fields, configured task
environment, status guards and current Codex/Claude dependency versions.
Cursor stays qualified. Copilot stays pending; profile 17 binds the
changed shared protocol validation sources.
- Exclude general AWS IAM credentials from Pi static/custom provider
bindings and selected task projections; preserve the provider-scoped
Bedrock bearer key. Profile 21 is retained as historical provenance.
Rust and cloud install probes use the current declaration.
- Patch bundled brace-expansion 5.0.9 to the exact official 5.0.12
payload. Pin the patch and complete runtime closures. Include the patch
in normal installed setup tooling. Keep the upstream Pi shrinkwrap as
provenance and permit only this exact security correction.
- Include current attestation files in the Docker build context. Keep
the repository lockfile unchanged from master. CI and private image
builds resolve manifest changes before their frozen installation.

## Verification

- Full local `pnpm -r typecheck` passes, including Runner Rust, server
and UI. Focused integration checks pass: 194 Runner
admission/environment tests, 63 profile/credential tests with one
expected skip, 152 Dot/UI configuration tests, and Pi transcript/notice
tests.
- Full local `pnpm build` passes on the final source.
- Fresh final-source checks pass: all 698 Rust workspace tests (32
binaries), 156 credential/profile/controller tests with one expected
skip, Runner TypeScript typecheck, and 20 package/setup/sandbox tests.
- The profile-21 Pi materializer passes on the native host with the
official pinned Node 24.21.0 and its npm. It verifies all 150 locked
packages, the patched dependency and the exact closure. Setup/package
bundle tests and UI token gates pass.
- The old hashes were reproduced for all three supported targets before
calculating the patched graph. New closure hashes are darwin-arm64
`282022db10150c6632b3444df421342e7d534bdf5d5fb1097a2e79d0625a2bcf`,
darwin-x64
`64e251e19009f755c0b04f73ce2138246faab71a961b0f13d75ebfcc34bef12e`, and
linux-x64
`713b1fdff42fb56a1518bdc084f181d70bee8ebadc3e4b1d76321ed9108c8410`.
Independent native platform execution is separate from graph identity
reproduction.
- Historical cloud qualification remains unchanged: all seven core cases
pass on shipping source `10dc43c9ec65d88c2f782d62afb296d09494f215`,
harness `1a4408a48cfb5a1f094a311141c257c92cd7a893`, image
`sha256:5b3a775b383591bda1b0c1889e509acc70ce7f37c53f09733c81d59037f02280`,
and accepted Sonnet 4.6/low fixture. All 215 canonical files and all
seven cleanup checks pass independent verification. These are profile-19
results and are not relabeled as fresh profile-22 runs.
- Current Pi digest:
`sha256:e92078bee3c23bec4100aa589013a44613d054cd686826534025d8019e9f39a9`.
[The readiness
plan](https://github.com/paperclipai/paperclip/blob/codex/pi-production-readiness/doc/plans/2026-10-02-pi-production-readiness.md)
preserves campaign and failed-attempt provenance.
- Merge only after every PR's current-head CI and fresh review pass.
Linux CI covers the full suites, build and browser tests. The local
embedded Postgres API-authority suite cannot start on this macOS/Node 26
host, so Linux CI must confirm that suite.

### Fresh profile-22 core qualification — 2026-10-08

All seven accepted core cases pass canonically on Pi profile 22, with
`openrouter/anthropic/claude-sonnet-4.6` and native-confirmed low
thinking. This model is a fixture; production accepts the caller's
explicit Pi provider/model.

Runtime/install source: `3241a992f2a7703e59e97ed0fd3e5d6405de4401`.
Frozen accepted harness: `1a4408a48cfb5a1f094a311141c257c92cd7a893`.
Immutable cloud image:
`ghcr.io/paperclipai/paperclip-daytona-runner@sha256:506f22db7edd78f37c0c40bec1cc084af1850455026dbf467194bfbb8fcef141`.
Pi digest:
`sha256:e92078bee3c23bec4100aa589013a44613d054cd686826534025d8019e9f39a9`.

[Hosted Linux image and clean-install
verification](https://github.com/paperclipai/paperclip/actions/runs/37868328023)
passes, including all 20 source-bound archives, normal CLI/Pi setup,
companion import and the production pack reader. This exact installation
source includes the latest master integration and the corrected Pi warm
instruction-root fence. Full local typecheck/build and current-head
hosted CI verify the final stack. All 13 focused real-root regressions
pass. The full local executor suite passed 662 tests; 15 database tests
could not start the Mac embedded PostgreSQL service. Hosted Linux CI
passes the full required verification and E2E checks. These fresh
results keep their own source identity; profile-19 results remain
historical.

| Core path | Canonical campaign | Retained archive SHA-256 |
| --- | --- | --- |
| File edit, validation, download and Done |
`pi-core22-replyfix-0-1791511228` | 23 files;
`a473e8603a3dd4737863291f8d3d1e392391f0b16d433c3e0e0e9d8baf7a97b0` |
| Pending question and controller restart |
`pi-core22-replyfix-1-1791511376` | 33 files;
`6b829c4eb74e1f32a89c692a4ae7130dbfc1c6d3cf13915effe2103d9e242c8e` |
| Three-turn session/process/workspace continuity |
`pi-core22-replyfix-2-1791511587` | 23 files;
`7a87021f8f9a3fdd3c58bb4467f8d82c635e3ea4795d6e75f144d9aa14818df8` |
| Four typed questions and browser reconnects |
`pi-core22-replyfix-3-1791511881` | 42 files;
`9e31755252be1f4f9cb0626c984c142d4d1ae5f5bee3a7af08444db8d12c280a` |
| Plan approval and completion | `pi-core22-replyfix-4-1791512031` | 22
files;
`a0383ce1aab38e7b5a25ce0e9dd3bebea5c037ebd96ae6b29dae19015da2ae2c` |
| Same-turn steering and permission denial |
`pi-core22-replyfix-5-1791512261` | 39 files;
`c929b8c7070f0b66aedc17e65ca46e6beab1e363926ac9f7e2a75fb250f05949` |
| Stop during pending permission | `pi-core22-replyfix-6-1791512390` |
33 files;
`7f0a58ae0f4d5bfc76149435f4e322537089c5bd16e7ffe9b5ad71f10a621a07` |

All 215 canonical files (28714587 bytes) are independently
hash-verified. All seven cleanup grades pass, with no owned runtime
process or temporary root after each case. Automatic retries are zero.
The owned cloud host stopped normally after retention. The prior
profile-22 warm attempt remains failed and separately retained: archive
SHA-256
`1e54eba5ec72b50cee1534b23d1d1d4f21a090006b8a64501ba70db972abfde5`. Its
original canonical classification is preserved. Diagnosis reproduced a
product bug comparing an agent-files root against an unset
checkpoint-only field. The fix stores the admitted physical root
separately from the adopted per-run collection capability. The real-root
regression fails before the fix and passes afterward, including
rejection of a changed physical root. Fixture, grader, model and all
seven accepted case IDs are unchanged; this fresh campaign tests
final-reply publication after file registration first. The intermediate
restart attempt also remains failed and retained: archive SHA-256
`5dcaefdf1d17cf4cd54fd4cf810f45e736667392339b8ce7caf08bb4e225277f`. Its
original canonical classification is preserved. Pi resumed, wrote the
verified answer and completed its task; exact runner suspension was
proven, but idle stop consumed about 5.2s and left under 3s for the
drain acknowledgement. The Pi-only default shutdown grace is now 15s,
preserving a full 5s drain round trip and a finite suspension reserve.
Explicit caller deadlines, other provider defaults, literal drain
receipts and exact suspension identity checks remain unchanged. The
timing regression fails before this correction and passes afterward; all
18 focused settlement tests and Runner typecheck pass. The final-source
file attempt is also preserved as failed (`candidate_failure`), archive
SHA-256
`db6767b6773ea618997927ac77bdb005a5ac81492c7b9c0ffbc900449f829bc9`.
Native edit, validation, exact downloadable artifact and Done/succeeded
all passed, and the exact final reply was durably recorded. A workspace
recovery owner completed before the live heartbeat reached presentation,
leaving that reply absent from task chat. Recovery now materializes only
a completed final reply from the accepted turn of an ordinary internal
Done task, preserving issue/run/contract binding, suppression,
external-chat authorization and same-run deduplication. The database
regression covers the generated file-preparation receipt, suppression,
unapproved external continuation and replay. Server typecheck and all 49
response-selection tests pass; hosted Linux verifies the database
regression because embedded PostgreSQL cannot start on this Mac.

The delayed-final-answer database regression passes on [the final
root-source Linux server
shard](https://github.com/paperclipai/paperclip/actions/runs/37868262553/job/113628594152),
alongside 1,108 passing tests. The first root Runner shard had one
unchanged durable-resume test exceed its 5-second timeout; the identical
top-source shard and the isolated exact test passed. One rerun of that
failed job and its required aggregate passed without source or test
changes. The original failed job log and the single-rerun receipt remain
retained.

### October 9 merge verification

Current merge head: `5a8fe63512a7166aaef5cf50065a25008aa8b44b`. All
current-head checks pass, including `ci / verify` and `ci / e2e`;
exact-head Greptile review is 5/5 with no unresolved threads. Current
master conflicts are resolved. The user authorized the maintainer
override of the code-owner review gate after these checks. The seven
retained live core cases remain bound to source
`3241a992f2a7703e59e97ed0fd3e5d6405de4401` and its recorded cloud image.

## Risks

- The security correction changes the dependency closure and profile
identity. Old sessions must reopen on the new profile. Exact identities
and credential bindings fail closed.
- The runner remains experimental and requires explicit selection.
Legacy Pi Local is unchanged. Caller model IDs pass through; the E2E
model is a fixture.
- Accounting and the broad platform/provider matrix remain deferred.
This merge does not publish a release or deploy a service.

## Model Used

OpenAI GPT-6 through Codex assisted with reasoning, repository
inspection, editing and tool use. The exact serving ID and context
window are not exposed in this session. Final live qualification uses Pi
1.0.0 with `openrouter/anthropic/claude-sonnet-4.6` and native-confirmed
low thinking.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` OR (b) described the issue in-PR following the relevant issue
template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
 2026-10-09 08:56:41 -05:00
DottaandPaperclip 1ead554bd1 fix(claude-local): resume sessions across agent file working copies (#15437) 
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The Claude CLI adapter resumes task sessions between runs.
> - Each run now receives a private copy of the agent files.
> - The adapter put that copy's path in the cached system instructions.
> - The new run ID changed the prompt bundle even when all instructions
and skills stayed the same.
> - This pull request sends the current file location with each run's
prompt and keeps it out of the stable bundle.
> - Agents can resume unchanged task sessions and use the current
working copy.

## Linked Issues or Issue Description

Fixes: #15373

Refs #14420, which introduced the per-run agent directory copies.
Related PRs checked: #5699 changes the fingerprint algorithm, and #12034
handles saved sessions without a bundle key. Neither fixes this
working-copy path regression.

## What Changed

- Keep instruction and skill contents in the cached system prompt.
Supply the current instruction path and relative-file base in every run
prompt, including resumed turns and fresh retries.
- Report a cwd or execution-target mismatch only when that value
differs. A bundle mismatch no longer produces a false cwd warning.
- Add a four-run regression: initial run, relocated copy, changed
instructions, and changed skill contents. Check the CLI arguments,
bundle keys, current file guidance, and reset logs.
- Cover and explain remote-to-local execution resets, even when the
working directory matches.
- Update the agent-file documentation and existing resume/fallback
assertions.

## Verification

- **Red:** With only the new regression test added, the second run fails
because the CLI arguments do not contain `--resume`.
- **Green:** All 64 tests pass in the command below. This uses a fake
Claude subprocess and real adapter execution, file caching, and session
serialization; it does not call a paid model.

```sh
pnpm exec vitest run server/src/__tests__/claude-local-execute.test.ts packages/adapters/claude-local/src/server/execute.remote.test.ts packages/adapters/claude-local/src/server/execute.acp-fallback.test.ts server/src/__tests__/adapter-session-codecs.test.ts
```

- Repository-wide `pnpm -r typecheck` and `pnpm build`: passed. The
adapter typecheck, build, and all 64 focused tests also pass after the
review fix.
- Local `pnpm test:run` was stopped after it reported a failure in the
unchanged native-session recovery database orchestration test. That test
passes in isolation with PostgreSQL enabled (1 passed, 47 filtered out).
The full local run did not complete; this is not a clean local
full-suite result. All CI checks pass on
`a71d23a39f1cc874d23a8715cf29bdea6edbb8ff`, including the full test
shards.

## Risks

- A session saved with the old path-bearing bundle starts fresh once
after upgrade. Later runs resume when instruction and skill contents
stay unchanged.
- The current location now travels in the run prompt. Stable system
guidance directs relative file references to that location, and each
turn explicitly replaces earlier locations.
- No database, API, authentication, permission, or UI change.

## Model Used

OpenAI Codex (GPT-6), with reasoning, repository inspection, code
execution, and test tools. The exact deployment model ID and context
window are not exposed in this session.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` OR (b) described the issue in-PR following the relevant issue
template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
 2026-10-07 06:48:19 -05:00
Devin FoleyandPaperclip d6d88b9de2 fix: preserve run outcomes when agent file cleanup is deferred (#14945) 
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - The heartbeat service records each agent turn and releases its
working files.
> - A turn can save its work and finish before instruction-copy cleanup
runs.
> - A cleanup exception can replace that completed result with an
adapter failure.
> - This also loses result accounting and can prevent environment lease
release.
> - This pull request records a cleanup warning and keeps the original
run outcome.
> - The existing recovery sweep retries cleanup from the durable
working-copy record.

## Linked Issues or Issue Description

Related cleanup and lock work: #14866 and #14869. Related, distinct
work: #14695 retains warm-process files; #12021 handles provider-process
SIGTERM after a terminal result.

**What happened?**

An agent saved its plan, posted a comment, and requested approval. The
provider completed its turn. Instruction-copy cleanup then timed out on
a directory lock. Its exception escaped a `finally` block and replaced
the provider result, so the completed turn showed `Run failed`.

**Expected behavior**

Keep the provider outcome, usage, cost, saved work, and pending
approval. Record a cleanup warning and let the existing recovery sweep
retry. A real provider failure must keep its original error. A failed
file save must keep its failed-save receipt.

**Steps to reproduce**

1. Complete a legacy adapter turn that saves work and requests approval.
2. Make instruction-copy release throw a directory-lock timeout.
3. Read the run result. Before this change, the cleanup error replaces
the provider outcome.

The new heartbeat tests reproduce the failure without a live provider or
external service.

**Paperclip version or commit**

The regression reproduces on `c83df091b1a5207375eaf23466bb5c62e4e1518e`.
This branch is rebased onto `cf8ad63c80`.

**Deployment mode**

Server-managed agent execution with persistent instruction working
copies.

## What Changed

- Catch instruction-copy release failures in both heartbeat teardown
paths. Stop repeating a failed cleanup attempt within the same run.
- Write a sanitized `instruction_cleanup` warning. A warning-write
failure also preserves the run result.
- Test successful, failed, and throwing providers; both teardown paths;
warning-write failure; accounting; approval state; and execution-control
release.
- Extend the held-lock test to prove a fresh recovery worker removes the
deferred copy and preserves its failed-save receipt.
- Document deferred cleanup and the run-log event.

## Verification

- Red proof: all five new heartbeat regression cases fail with the
original release calls.
- At head `20bea4f431c916d2f5db1970213aab85f5daa34c`, all 417 tests
passed across heartbeat process recovery, agent directory working
copies, and directory merge locks.
- Full local `pnpm -r typecheck`, `pnpm build`, and `git diff --check`
passed.
- [GitHub
CI](https://github.com/paperclipai/paperclip/actions/runs/37031119795)
passed at this head. All 53 reported checks passed; the two Storybook
checks were correctly skipped. This includes general and serialized
tests, browser shards, runner verification, build, typecheck, and the
canary dry run.
- Greptile reviewed this head with 5/5, no code comments, and no
unresolved review threads. The branch has no merge conflicts.
- The local `pnpm test:run` attempt was stopped after it reported eight
failures in unchanged suites. Four Slack/AgentMail cases selected an
unrelated ancestor skills directory and failed with `ENOENT`; the two
Slack cases passed with a temporary local skill-root link, which was
then removed. Three company-skill cases reproduced macOS `EACCES` errors
when renaming read-only cache directories. One gateway case passed when
rerun alone. No full local-suite pass is claimed; the complete CI test
jobs passed.

## Risks

- Cleanup errors now leave recovery work pending. The durable
working-copy record remains available for the existing retry sweep.
- This change preserves provider failures and failed-save receipts. It
does not claim that unsaved file edits were saved.
- Native instruction reservation errors retain their existing behavior
because they guard process ownership.
- No schema, lockfile, workflow, API, or UI changes.

## Model Used

OpenAI Codex, based on GPT-6, with reasoning, repository tools, and code
execution. The exact backend model ID and context-window size are not
exposed by this session.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

Co-authored-by: Paperclip <noreply@paperclip.ing>
 2026-10-02 14:16:18 -07:00
Devin FoleyandPaperclip f2e0f19630 Defer agent directory cleanup until stop proof is available (#14866) 
## Thinking Path

> - Paperclip manages agents and their persistent files.
> - Each run owns a temporary agent directory and a save receipt.
> - Cleanup needs independent proof that the owning process stopped.
> - A cleanup call without that proof currently waits for the directory
lock anyway.
> - A second lock failure can prevent environment release after the run
already reported a failed save.
> - This change skips cleanup that has no authority and retries
unavailable remote copies after exact destruction proof.
> - The save failure stays visible. Existing lock owners remain
protected.

## Linked Issues or Issue Description

Related work: Refs #14787 (lock diagnostics), #14695 (warm instruction
ownership), #9667 (stale lock proposal), and #9872 (control-plane
ownership proposal). I checked open PRs and issues. This change leaves
the shared filesystem lock protocol in place and does not duplicate the
warm-retention work in #14695.

**What happened?**

Heartbeat cleanup records an explicit unavailable instruction-save
warning, then calls directory release before releasing the environment
lease. Release can wait for a lock even though the copy has no
process-stop proof and cannot be removed. That secondary timeout
prevents the following lease-release step. If destruction proof arrives
later, the unavailable copy is excluded from both recovery queries.

**Expected behavior**

Skip a release that cannot remove anything. Preserve the failed-save
receipt and candidate fields. Once exact remote destruction is recorded,
recover remote cleanup without running a provider command. Unavailable
local copies retain their potentially uncollected edits even if local
stop proof arrives later. A blocked cleanup must not prevent cleanup for
other agents.

**Steps to reproduce**

1. Prepare an agent directory, report its save unavailable, and leave
process-stop proof absent.
2. Hold the shared directory lock and call release. Before this change,
release waits and fails although removal is not authorized.
3. Record destruction of the copy's exact remote lease. Before this
change, neither recovery sweep selects the unavailable copy.

**Paperclip version or commit**

Reproduced against `efc2e6810e9bc0dc8cb412b0e7647c0db9821caa`.

**Deployment mode**

Local and remote execution with persistent agent directories. Tests use
an isolated embedded PostgreSQL database and fixture transports.

## What Changed

- Re-read receipts and skip release before lock acquisition when stop
proof is absent, the copy is superseded, or cleanup is complete. Keep
the same checks inside the lock.
- Recover unavailable remote copies only after exact destruction proof.
Preserve their unavailable state, errors, candidate hash, and candidate
bytes. Keep unavailable local copies and their uncollected edits
unchanged.
- Store destruction-only cleanup authority with the stop proof. Later
cleanup honors it after a lost database response or restart, including
when a transport remains cached.
- Defer failed or unproven cleanup with bounded batches and a retry
delay. Keep failed cleanup visible in logs and its receipt.
- Serialize preparation of an existing run with cleanup. Fresh run
preparation keeps its existing admission path.
- Cover held locks, receipt scope, delayed proof, batch fairness, lost
update responses, cached transports, and concurrent same-run preparation
with database regressions.

## Verification

- Focused directory, legacy instruction-copy, shared lock, and bounded
diagnostic suites: 169 tests passed across four files.
- `pnpm -r typecheck`: passed on the final source.
- `pnpm build`: passed on the final source.
- Completed all selected local `pnpm test:run` groups: 733 general
server suites, 149 serialized suites, and 14 workspace projects. There
are 13 known macOS `EACCES` failures in the unchanged runtime skill
cache tests. Their exact signatures match earlier clean-base results,
and the cache source and test blobs match both that base and this PR
base (existing fix: #14290). One CLI import test timed out under
concurrent load; its full file passed separately (17 tests). Broad
coverage began before the review corrections; the final source has the
focused 169-test run, typecheck, and build. This is a local verification
limit, not a passing full local suite.
- `git diff --check` and local Gitleaks plus private-identifier/PII diff
scans passed.
- Independent review of the final source found no remaining actionable
issue. Its 17 targeted tests cover crash recovery, cached transports,
same-run preparation, real local edit preservation, proof scope, and
batch fairness. The main focused run also covers contained scheduling
failures.
- Final commit `35a24085f7`: Greptile 5/5 with no recommendations and
zero unresolved review threads.
- Final commit `35a24085f7`: all 53 checks passed, including Canary Dry
Run and the security scan; two visual checks were intentionally skipped.
The workspace shard passed on retry after GitHub reported that its first
runner lost communication. An earlier Canary runner shut down after the
release dry run passed. Neither interruption recorded an application
assertion failure; the exact final-head checks are now green.

## Risks

- This repairs cleanup ordering and recovery eligibility. It does not
repair an ambiguous legacy lock owner or restore unsaved files. Actual
collection still fails visibly when its lock cannot be acquired.
- An unavailable remote copy is recovered only after exact destruction
proof. A stopped but retained environment stays protected; recovery does
not execute a command that could restart it.
- Unavailable local copies with later stop proof still retain
potentially uncollected edits. A general local recollection or
reclamation policy remains outside this change.
- Existing-run preparation now waits for the same lock as cleanup. The
fresh-run path is unchanged.
- The cleanup mode is stored in the existing private receipt JSON. No
schema migration or public API change is required.
- No deployment, task replay, or runtime lock deletion was performed.

## Model Used

OpenAI GPT-6 (Codex), with reasoning, repository tools, and test
execution. The runtime does not expose a more specific model suffix or
context-window size.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` OR (b) described the issue in-PR following the relevant issue
template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub references)
- [x] My branch name describes the change and contains no internal
Paperclip ticket id
- [ ] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
 2026-10-01 14:28:47 -07:00
DottaandPaperclip b54b2dc35c fix: preserve warm Codex turns with incremental managed file checkpoints (#14735) 
## Thinking Path

> - Paperclip manages AI agents and keeps their instructions and files
durable.
> - Native Codex runners can keep a process alive between compatible
turns.
> - Managed file collection stopped that process after each turn, which
defeated warm reuse.
> - Agent folders can contain large images and other files, so full
copies on every turn are expensive.
> - This change keeps one managed directory for the live session and
saves only file changes after each turn.
> - Ownership, authorization, instruction changes, and process
retirement still control when reuse is safe.

## Linked Issues or Issue Description

Related: #13710 introduced native warm session reuse. This fixes managed
file collection that still forced those sessions to stop. No duplicate
open PR or issue was found.

**What happened?**

With managed instructions and warm native Codex enabled, consecutive
turns reused a Daytona sandbox but started a new runner process each
time. The managed directory collector required process termination
before saving files.

**Expected behavior**

Compatible turns keep the same process and managed `AGENT_HOME`. Each
completed turn saves added, changed, and deleted files before the next
turn starts. Unchanged large files do not transfer again.

**Steps to reproduce**

1. Use a native Codex agent with managed instructions and a reusable
Daytona environment.
2. Enable warm session reuse and run three turns on the same task.
3. Write a large binary on the first turn, edit a small note on each
turn, and delete a file on the second turn.
4. Compare process identity across turns and read the canonical files
through the public agent-files API.

**Paperclip version or commit**

Reproduced on `d30b03bd8c17604cdab1533eeeeb087aba30e8b1`.

**Deployment mode**

Local server with remote Daytona execution; cloud native runner uses the
same path.

## What Changed

- Retain the managed directory only for the verified owner of a live
native Codex session.
- Checkpoint each completed turn before releasing the session for reuse.
Retry unstable captures, then stop and collect when a warm checkpoint
cannot be validated.
- Compare metadata and cached hashes, stream only changed file payloads,
record deletions, and validate path, content, quota, and authorization
before saving.
- Rotate sessions when canonical files, loaded instructions,
credentials, or launch policy change. Fence stale collection and cleanup
callbacks from later owners.
- Keep cleanup and recovery aware of the current session owner. Recheck
canonical files under the writer lock at handoff, attach the successor
collector before fallible bookkeeping, and emit one final save receipt
on checkpoint fallback. Preserve storage warnings across unchanged
checkpoints.
- Add regression coverage and a three-turn Daytona test with independent
public API file checks, an unchanged 8 MiB binary, deletion checks, and
strict process identity checks.
- Document checkpoint consistency, lifecycle behavior, and local run-log
counters.
- Replace a timing assumption in the Daytona teardown test with explicit
transfer-arrival gates after CI exposed an unset release callback.

## Verification

- Full local `pnpm -r typecheck` and `pnpm build` passed. Server checks
were repeated after the final storage-warning fix.
- Runner E2E typecheck and 749 runner E2E unit tests passed.
- Focused file checkpoint, directory ownership, instruction collection,
native session, and merge tests passed. After review fixes, the
managed-directory and native-session suites passed 550 tests, including
intervening canonical edits, same-run fresh restore, failed handoff
collection, and one-call fallback collection. Server typecheck passed
again. The Daytona plugin suite passed 218 tests. The quota-warning
regression failed before the fix and passed afterward.
- Three real Daytona campaigns passed before the final handoff review
fixes. The latest kept PID 547 across all three turns. The first
checkpoint copied 8,388,635 bytes; the next two copied 36 and 54 bytes.
Public API reads verified the binary, note contents, and deletion after
every turn. Test cleanup deleted the sandbox.
- The final head was also deployed to an isolated cloud staging instance
and passed three UI-triggered native Codex turns with managed
instructions. All three retained the same process ID/start time, native
session, provider session, runner instance, and Daytona sandbox.
Checkpoints copied 8,388,643 bytes on turn 1, then only 52 and 78 bytes
on turns 2 and 3; those warm captures also hashed only 52 and 78 bytes.
Independent canonical API reads verified every byte of the unchanged 8
MiB binary and the exact note contents after every turn; the deleted
file returned 404 after turns 2 and 3. After restoring the original
lifecycle and agent-auth configuration, removing the temporary secret,
pausing the test agent, and deleting both test sandboxes, independent
canonical API reads still verified the entire binary, the final 78-byte
three-line note, and the deletion. The native runner flag remained
enabled and the final serving revision remained the PR head.
- Two earlier staging attempts are preserved as failures and are
excluded from the acceptance result: a saved ChatGPT login failed with a
provider routing 401, and its subsequent stopped-sandbox retry failed
before provider startup with a closed-lease admission error. The
successful campaign used a fresh sandbox and a temporary encrypted
API-key binding. The stopped-lease retry remains unexplained; this
campaign does not establish recovery of that failed sandbox.
- All [Paperclip CI
gates](https://github.com/paperclipai/paperclip/actions/runs/36750397355)
pass on `26ef2ef56a389259246809805c0b34a4747eb86b`, including full test
partitions, build, typecheck, runner verification, E2E shards, and the
Canary clean public-npm install. Greptile reviewed that exact head at
5/5 with no unresolved review threads or outstanding findings.
- Full local repository coverage used the existing CI partitions, but
the 40,000-file Git streaming stress test timed out and its local retry
was interrupted by macOS thermal emergency sleep; this is not a green
full local suite claim. The exact stress test passed on the final head
in [CI server shard
2/12](https://github.com/paperclipai/paperclip/actions/runs/36750397355/job/110008294290),
in 111.9 seconds.
- Repeat the live test with configured credentials and a Linux runner
artifact: `pnpm test:e2e:runner -- --id
daytona-warm-continuity.runner-codex.daytona.warm-three-turn`.

## Risks

- This is a file-level checkpoint, not an atomic snapshot of the whole
folder. Background writes after a capture are saved by the next
checkpoint or final stopped collection.
- Metadata scans still visit all paths. Modified files transfer in full;
unchanged files do not rehash or transfer.
- Incorrect ownership or reuse could collect the wrong directory. Run
ownership fences, current authorization, stable capture validation, and
stopped collection fallbacks are covered by tests.
- Warm reuse remains opt-in. No database migration or fleet default
changes.

## Model Used

OpenAI GPT-6 through Codex, with reasoning, code editing, tool use, and
test execution. The exact serving model ID and context-window size are
not exposed by this session.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
 2026-09-30 13:33:37 -05:00
DottaandFry 3ca196b0a6 feat(agents): persist agent files across tasks without revision history (#14420) 
## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - An agent needs personal files across tasks and sessions.
> - AGENTS.md is one file in that directory. Supporting files need the
same persistence.
> - The Instructions Editor and agent runs must share one current
directory.
> - Concurrent runs should apply only the files they change. The last
sync of the same file wins.
> - This pull request uses existing file transport and removes temporary
copies after sync.
> - Old instruction-only sessions keep their restore contract. New saves
do not create revision history.

## Linked Issues or Issue Description

Refs #14325. This replaces its revision-oriented design with persistent
agent files. Keep #14325 unmerged.

Transport prerequisite #14416 merged first at
`d172197117a14b80a1eb2d2835a0e7cce2679656`. This PR now targets master
and remains below 100 changed files.

Related work: #4513 and #8798 cover instruction tooling. This change
handles run synchronization, cross-task personal files, browser editing,
and old-session restoration.

## What Changed

- Keep one current directory per company and agent. Point AGENT_HOME at
a temporary working copy for each active run. Keep task files and
provider HOME separate.
- Restore text, binary files, and nested folders through workspace
transport. Exclude remote agent files from task Git snapshots with a
self-ignoring file inside the reserved runtime directory; never write
through repository-controlled Git metadata.
- Collect after the provider and child processes have stopped. Keep
resumable conversation state.
- Apply changed and deleted files under the agent lock. The last sync
wins for the same file. Unrelated concurrent changes survive.
- Remove temporary copies after successful sync, rejected sync, and
staging failure. Register ownership before copying so restart recovery
can remove interrupted preparation. Retry transient synchronization up
to three times. Preserve the original remote lease reference until
deletion succeeds; restart cleanup never acquires a replacement sandbox.
Do not create captured directories or a conflict-review queue for new
runs.
- Keep browser editing, stale-draft protection, and streaming binary
downloads. Keep the instruction entry and text editor limited to 1 MiB.
- Keep historical agent-folder sync failures on their affected runs
instead of repeating them above current saved instructions. Preserve
legacy candidate review and current browser-save errors. Avoid duplicate
quota warnings while retaining separate sync failures when they describe
a different problem.
- Require target-scoped caller grants for peer instruction access, while
preserving self edits, responsible-user checks, and protected-change
consent.
- Treat full storage as a nonblocking run warning, never an agent pause
or run-admission failure. Restore already-over-quota saved folders so
ordinary agent cleanup can recover; warn on each run until cleanup. The
run detail view shows the warning.
- Allow 256 MiB per file, 2 GiB per directory, and 100,000 entries. Hash
large files as streams. Check editor-save quotas with metadata instead
of hashing unrelated files.
- Preserve old native inputs, instruction-only copies, paths, digests,
and pending legacy candidates. Adopt old revision heads once. New writes
do not append history rows.
- Add idempotent migration 0287 and verify upgrades from the preview
tables and receipts.
- Add nine interactive stories under **Agents / Persistent files**,
including automatic incoming edits, stale browser drafts, and
storage-limit diagnostics.

## Verification

- Merge candidate: `4f5390107ec6ffd80a76d1d2e85530e66f21d079`, after
merging current master and the landed transport prerequisite.
Integration required no manual conflict resolution; the feature remains
99 changed files. Full workspace typecheck, production build, token
gates, and 715 focused tests passed on this merge candidate. Fresh
Greptile review is 5/5 with no unresolved findings. All 55 checks
passed, with four conditional skips, including the build, typecheck,
browser E2E, and canary dry run. A single retry recovered four jobs
interrupted by runner shutdowns; no source changes were required.
- Historical-warning UI fix: all 6,834 UI tests across 640 files passed,
including regression coverage for three old failures, legacy preserved
edits, and warnings scoped to the affected run. Full workspace
typecheck, production build, Storybook build, and token gates passed.
Browser-verified Storybook playtests passed for Historical Failures
After Successful Save, Storage Limit, and Full Storage Run Warning.
- Review follow-ups at `4e20c9fb2`: all 18 focused tests passed,
including external Git directories, linked worktrees, symlinks,
hardlinks, and distinct I/O failures alongside storage warnings. Server
and UI typechecks, token gates, and the production build passed.
- Storage warning regressions at `0724f3012`: all 33 directory tests and
all five heartbeat-list tests passed, with no skips in their successful
runs. They cover repeated runs while full, an already-over-quota saved
folder, cleanup, warnings retained after unrelated save failures, and
bounded warnings in large result JSON. Server typecheck passed after the
final warning fixes.
- Full workspace typecheck, production build, and token gates passed
during this follow-up. Product E2E harness: 631 tests passed across 52
files; harness typecheck passed. Earlier native session/context and
directory/legacy collection suites passed 537 tests; Runner
unit/transport suites passed 329 tests.
- **Real E2E at `0724f3012` (before this follow-up):** legacy local
Codex and native Daytona Codex each passed six tasks, one server
restart, seven independent assertions, and cleanup verification. Both
prove browser-to-agent edits, agent-to-browser edits, nested/binary
restoration, per-file last-sync-wins, a successful run after an
oversized save rejection, and cleanup clearing the warning.
- Native local Codex also passed the six-task quota flow before the
final warning-retention fixes. That pass began at `918d1ed02` while the
bounded-result warning fix was being edited, so it is not claimed as
exact-final-head evidence. Its final-head rerun failed during embedded
PostgreSQL bootstrap before any provider run: the macOS host had 87,365
of 87,381 SysV semaphores occupied. No unrelated services or kernel
limits were changed.
- The final-source report intentionally records **2/3 cells passed**,
preserving the blocked native-local attempt:
`tests/runner-e2e/results/agent-files-quota-final-20260928-report/`.
Earlier failed attempts and provenance notes remain under
`tests/runner-e2e/results/agent-files-quota-final-20260928-input/` and
the original campaign directories.
- Daytona used immutable image
`ghcr.io/paperclipai/paperclip-daytona-runner@sha256:5643f0d801417cae3581833a1a3bc6715b325e028602738d2652c44cac5dc6bf`
and its exact Linux runner binary. Controller source is `0724f3012`;
image source is recorded separately.
- Legacy-session compatibility and all three ACP Stop/resume browser
regressions passed on the prior validated feature head
`169fab46d5af21caa2269b4c1b29b69c933a6951`. They assert the same
provider session is retained and interrupted writes are not replayed.
Migration upgrade tests also passed earlier.
- Nine interactive stories are under **Agents / Persistent files**,
including **Full Storage Run Warning**. Its playtest and visual browser
inspection passed; the warning states that runs continue and the editor
remains available.
- Prior-head checks on `4e20c9fb2`: 55 passed, two conditional jobs
skipped, no failures or pending checks. All eight browser E2E shards and
their aggregate passed. Fresh Greptile review is 5/5 with no findings;
all review threads are resolved, the security scan passed, and GitHub
reports no merge conflicts.
- The broad local follow-up test run was interrupted after host
semaphore exhaustion affected isolated PostgreSQL instances. It also
encountered the existing macOS long-path fixture failure and two timeout
failures. This is not a claim that the full local suite passed. Logs are
retained; focused storage/warning tests passed.

## Risks

- A later sync can overwrite an earlier edit to the same file, including
a saved browser edit. There is no text merge or retained version. This
is the intended last-sync-wins policy.
- A save that exceeds a storage limit is rejected and its temporary copy
is discarded. The run itself continues normally, and later runs restore
the last saved files with a warning until cleanup. Transient sync
failures get bounded retries. An I/O failure partway through a sync can
leave some files updated; a failed receipt does not claim whole-folder
success.
- Larger folders increase copy time, network traffic, and temporary disk
usage. Active runs still need working copies. Terminal runs do not
accumulate archives. Operators must provision disk for agents and
configured concurrency; these limits are not company-wide quotas.
- A restored old native session remains instruction-only until a fresh
session starts. Its original conflict fence and existing pending
candidates remain compatible.
- Provider processes close at the collection boundary. Conversation
resume remains available, but warm process reuse is lost.
- Backups must include the instance filesystem and database. External
bundles keep their existing behavior until explicitly moved to managed
storage.

## Model Used

OpenAI Codex, GPT-6 family. The session does not expose a more specific
model ID or context-window size. Reasoning, code execution, and browser
tools assisted this change. Real provider E2E uses `gpt-5.6-sol`.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Fry (Paperclip) <noreply@paperclip.ing>
 2026-09-29 08:25:56 -05:00