2 Commits

Include renames

Author	SHA1	Message	Date
Dotta	a9830414c7	Preserve repository dependencies when importing GitHub skills (#15731) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Its Skills library imports reusable instructions from GitHub. > - Some skills depend on shared files and sibling skills outside their folders. > - Directory-only imports lose those dependencies. > - This pull request keeps repository files together and lets users select which skills appear in the library. > - Agents receive the original files and paths through the existing skill delivery system. ## Linked Issues or Issue Description Refs #14713. Related: #13656. **Current behavior** GitHub imports copy independent skill directories. Shared scripts, policies, helper skills, and credit files can be omitted. One shared-file error can block every skill. **Proposed behavior** New imports keep repository files together at the scanned commit. Show all skills with their folders and select every skill by default. Collapse individual package files. Omit unsupported or oversized files with a warning. Import available content without repair choices or an extra confirmation. Keep warnings on the saved source. **Reason and benefit** Skills can read their shared repository files after Paperclip delivers them to an agent. Original instructions stay unchanged. Users can inspect included files and understand omissions before and after import. ## What Changed - Store immutable company-scoped repository snapshots and associate them with skill versions. Regenerate the migration after merging master. - Preserve original bytes, binary encoding, and executable modes. Shared-file changes version each usable selected skill. Pinned versions retain their original files. - Deliver a discovery wrapper with the original tree under `.paperclip-repository/`. Preserve invocation policy when present. Fork and create-from-existing retain repository files. - Keep repository files together for new UI imports. Show every skill, select all by default, and collapse package files. Remove the packaging-mode menu. Keep the mobile import footer visible. - Warn about symlinks, submodules, oversized files, missing references, and invalid optional manifests. A malformed skill remains selected with a Needs setup warning. Usable skills still publish, and its original file remains repository support content. Source warnings persist through refresh. Unsafe execution and secret-disclosure findings omit the affected files before snapshot publication. - Expose saved repository files in the installed skill viewer, including binary encoding and executable flags. Reads use the immutable company-scoped snapshot; relative instruction links resolve from their original repository directory. - Audit delivered inventories and derive trust from all repository files. Accept evaluation prose while retaining dynamic-execution findings. Read blobs in one bounded Git batch and check budgets before reading support files. Imports never execute setup commands. - Add scanner, database, delivery, UI, and browser regressions. Update Storybooks, screenshots, and documentation. ## Verification - 69 focused scanner, Git snapshot, delivery, and PostgreSQL lifecycle tests passed. They cover partial imports, warning persistence, missing references, binary files, executable modes, copies, pinned versions, cancellation, company isolation, and batched Git reads. - 110 import, skill-detail, selection-tree, saved-file link, and Markdown renderer tests passed. A file-switch regression failed before the resolver fix and passed afterward. Browser walkthroughs cover the all-selected open tree, repository preview, non-blocking warnings, missing references, setup problems, warning persistence, and mobile layout. - Full workspace typecheck and build passed. Runner E2E TypeScript checks and design-token gates passed. The full serial local suite was attempted and stopped after over an hour. The existing 40,000-file Git streaming stress test failed after 303 seconds on macOS; the broad local suite is not counted as passed. All 55 applicable PR checks passed on the final commit, including the full sharded CI suite. Two optional Storybook workflows were skipped; the five local Storybook walkthroughs passed. - On October 12, live campaigns imported the private Poteto repository through the production GitHub Sources UI, selected architect and bro, and invoked them with native Codex on local and Daytona. The source connection was disabled before invocation. Independent filesystem inspections matched every supported Git blob, size, and executable mode. Both tasks completed and cleanup passed. Campaigns: `local-2026-10-12T15-07-39-504Z` (both environments), `local-2026-10-12T16-08-39-682Z` (local), and `local-2026-10-12T16-03-33-938Z` (Daytona). Each of the two selected skills received all 234 supported repository files. Later changes only affect the installed-file viewer and documentation. This qualifies skill delivery and instruction reads, not every Poteto workflow or adapter. - A manual source-checkout test drive imported a synthetic private GitHub repository with a symlink, an oversized file, a missing reference, and malformed skill metadata. Available skills published with their shared checklist. The walkthrough found duplicate warning text after import; the final UI fix removes that duplicate. The file viewer exposes saved repository dependencies and resolves authored relative links without changing the instructions. A follow-up live refresh omitted unsafe helper files with warnings, preserved every safe file byte, and survived a server restart. Screenshots below use the production UI with Storybook fixtures. They do not replace the live GitHub and runtime checks. <details> <summary>All skills visible and selected by default</summary>  </details> <details> <summary>Import stays available with warnings</summary>  </details> <details> <summary>Repository file inspector</summary>  </details> <details> <summary>Mobile import</summary>  </details> ## Risks - Each selected skill carries a repository copy in the runtime. The database stores each snapshot once. Runtime transfer and storage increase with the number of assigned skills. - Runtime budgets remain: 9,990 repository entries, 1 MiB per file, and 61 MiB total. File omissions are recorded as warnings. Source-access or download failures retain installed versions. - Import success does not prove that every skill can run. Environment dependencies, credentials, delegation tools, and schedules still need configuration. Imported setup scripts are not executed. - Live runtime coverage is native Codex on local and Daytona. Other adapters use the shared delivery path but were not exercised in these campaigns. The roadmap marks Skills Manager as shipped. This extends the existing importer. Related pull requests were checked. ## Model Used OpenAI Codex, based on GPT-6, with repository inspection, code execution, automated tests, and browser tools. The exact deployment identifier and context-window size were 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 #` / `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 - [ ] 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	2026-10-12 11:30:20 -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