4 Commits

Include renames

Author	SHA1	Message	Date
3 people	81cea89d6b	fix(cli): require confirmation for instructions file deletes (#11504) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - The CLI exposes board/operator controls for managing agent configuration and instructions. > - Agent instructions files influence future agent behavior, so deleting one is a destructive configuration mutation. > - Nearby destructive CLI commands already require explicit `--yes` confirmation before sending DELETE requests. > - `agent instructions-file:delete` skipped that local confirmation guard and could delete a bundle file from a scripted or mistyped command. > - This pull request aligns that command with the existing destructive-command safety convention. > - The benefit is a small, predictable operator-safety guard with focused regression coverage. ## Linked Issues or Issue Description Bug report: ### Pre-submission checklist - [x] I have searched existing open and closed issues and this is not a duplicate. - [x] I am on the latest released version of Paperclip (or can reproduce on `master`). - [x] I have confirmed the error originates in Paperclip itself — not in my agent adapter, API provider, or local configuration. ### What happened? `paperclipai agent instructions-file:delete` deleted an agent instructions bundle file without requiring explicit CLI confirmation. ### Expected behavior Destructive CLI delete operations should require `--yes` before sending a DELETE request. ### Steps to reproduce 1. Run `npx paperclipai agent instructions-file:delete <agent-id> --path AGENTS.md`. 2. Observe that the CLI immediately issues `DELETE /api/agents/:agentId/instructions-bundle/file?path=AGENTS.md`. 3. No local confirmation guard blocks the destructive request. ### Paperclip version or commit `fd472d02ba950519ca5eff75ed9fd55cf976f4c2` ### Deployment mode Local dev (`pnpm dev`) ### Installation method Built from source (`pnpm dev` / `pnpm build`) ### Agent adapter(s) involved - [x] Not adapter-specific (core bug) ### Database mode Not database-related ### Access context Board (human operator) ### Node.js version `v20.x` ### Operating system macOS ### Relevant logs or output ```text Current behavior is local CLI behavior: the command proceeds to the DELETE call without requiring `--yes`. ``` ### Relevant config (if applicable) None. ### Additional context This command already sits next to other destructive CLI actions such as `agent delete`, which require explicit confirmation. Aligning the guard makes the CLI safety model consistent. ### Privacy checklist - [x] I have reviewed all pasted output for PII (usernames, file paths, API keys, tokens, company names) and redacted where necessary. ## What Changed - Added a `--yes` confirmation option to `agent instructions-file:delete`. - Refuse the command locally before resolving API context or sending a DELETE request when confirmation is missing. - Updated CLI parity coverage for confirmed and refused instructions-file deletion. - Updated the CLI documentation example to include `--yes`. ## Verification - `/Users/xinran/Downloads/dev/paperclip-pr-work/node_modules/.bin/vitest run cli/src/__tests__/agent-lifecycle.test.ts --config cli/vitest.config.ts` equivalent executed from the PR worktree using temporary dependency symlinks: 3 tests passed. - `git diff --check` ## Risks - Low risk: this only changes one destructive CLI command and matches existing `agent delete`, `issue delete`, and other delete-command confirmation behavior. - Scripts that intentionally delete instructions files must add `--yes`, which is the intended explicit confirmation path. - No database, API contract, or lockfile changes. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - OpenAI Codex, GPT-5-based coding agent in Codex desktop with shell/tool use and local test execution. ## 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 - [ ] All Paperclip CI gates are green - [ ] 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: 馨冉 <xinxincui239@gmail.com> Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-15 15:36:23 -07:00
DottaandPaperclip	adb69e8f09	feat: default new Codex agents to Paperclip Runner on Linux and macOS (#15683) ... ## Thinking Path > - Paperclip is the open source control plane for agent companies. > - People choose a harness when creating an agent. > - The server should resolve that harness to a qualified runner. > - Codex is the first harness in the staged default rollout. > - Saved agents must retain their execution choices. > - New Codex agents therefore use Paperclip Runner on qualified macOS/Linux targets, with an explicit Legacy override. ## Linked Issues or Issue Description Refs #16028, #15555, #15673, #15422, #15631, #15926, #15932, #16149. The runtime/install prerequisite and release repair are merged. This slice owns Codex creation, setup, configuration and preservation. Other harness defaults remain unchanged. It adds no database migration; incoming master migrations, required maps and regression coverage are retained. ## What Changed - Resolve `runner: auto | paperclip | legacy` at the common creation boundary across onboarding, API/CLI, hires, built-ins, plugins and imports. Freeze pending hires and export resolved execution choices. - Preserve existing runners on upgrades, unrelated edits and import updates, including compatible accounts, workspace settings, Codex effort and intentional clears. - Use the underlying harness picker and branding; put the runner override in Advanced. Use the shared dropdown and update production-component stories and creation contracts. - Support qualified Apple Silicon, Intel Mac, Linux x64 and Linux ARM64. Linux requires GNU libc 2.39+. Disabled, external, unsupported and unqualified combinations retain their applicable Legacy execution. - Test the selected runtime/account/model/environment. Ordinary Connect probes eligible immutable managed targets and refreshes scoped discovery. Creation/discovery do not provision. Auth, dependency, incompatible-setting and cleanup failures remain actionable without changing runners. - Keep setup probes read-only, preserve local/SSH isolation and resolve packaged assets before staging credentials. Bound cleanup reads by the remaining absolute deadline; physically close every owned ingress socket before endpoint release. Unconfirmed cleanup retains recovery state. - Preserve validated completed-onboarding callbacks through startup recovery. First file-producing work belongs to the child task and uses the existing dependency/block handoff and task-scoped registration. - Reuse existing E2E fixtures, artifact checks, reporting and controls. Keep Docker/Cargo/native compilation remote. Paperclip tarballs contain no Codex payloads; official optional npm platform dependencies remain. ## Verification Current tested head: `1c03a8815672d82c264a9b08d4ea1984e8fae107`. **Merge-ready: required CI, fresh review, package qualification, Mac core acceptance and Test task/follow-up acceptance pass.** The existing attachment and native-continuity oracles independently verify both Test downloads, run attribution and unchanged native/provider/workspace identities. The maintainer authorized a code-owner-review exception for this PR only. The first Test setup failure and normal Board completion-review friction are retained below. Actual post-merge packages and private Cloud distribution remain separate qualification gates. - [Current CI](https://github.com/paperclipai/paperclip/actions/runs/38564241625): all 48 ordinary jobs and required verify/E2E pass. Attempt 1 retained six simultaneous host-shutdown cancellations. One failed-only retry passes those six lanes and two aggregates, preserving 40 successes. Actual integration checkout `53104c1` combines this head with master `c80`; it is not relabeled as the branch tree. Fresh exact-head Greptile 5/5, 30 resolved threads, no actionable findings. - [Exact-source package qualification](https://github.com/paperclipai/paperclip/actions/runs/38565287239): nine applicable jobs pass, nine conditional jobs skip. Four remote native producers; Linux x64 clean install; Intel Mac, Apple Silicon and Linux ARM64 native startup/physical cleanup controls. All 18 tarballs/four daemon source/hash/manifest bindings and 343 migrations through 0344 verify. No Codex payload is packed. These hosted tarballs are not a published npm canary. - Normal Apple Silicon installation and credential-free native startup/cleanup pass using the packaged daemon, with no source build or provider turn. Fresh installed DB initialization passes. Upgrade 651a→1c03 preserves all three complete execution configs, accounts, ten recorded run profiles, paused budgets, active incidents, cost summaries and two historical unpriced events. Historical recovery state is retained. - Cleanup regressions: four delayed-read baseline failures become 15 passing deadline/authority controls. No-acknowledgement and prior-error socket ownership regressions become 12 passing controls. Direct runtime/server types, maps: 35 areas / 176 IDs, diff checks and independent reviews pass. Permission/auth/reconnect policy and the 10-second setup budget remain intact. - Existing source coverage includes creation/selection/imports, pending approvals, recovery, account/lifecycle handling, mounted forms, dropdowns and E2E support. Full typechecks/tests/build/token and applicable Storybook checks pass in the recorded current CI; no duplicate suite or weakened grader. - Literal 9546 live Mac proof: ordinary Auto Codex onboarding, useful document, real completed-child callback/reply, seven successful native runs, manual follow-up and independently downloaded1,101-byte child file. Existing Legacy title edit/reload preserves execution; two real Legacy runs produce independently checked15/34-byte files. These remain historical source records. - Current literal 1c03 Mac core acceptance passes independent checks: ordinary Auto native Codex onboarding without runner override; only timeout 180 seconds/concurrency 1 saved; six successful native runs and six serialized turns (maximum overlap 1); both same-task continuity checks and five mechanical callback checks; actual rendered parent reply and exact child downloads. The useful handoff advances from revision 1 to 2. Both files are 48 bytes, SHA-256 `8b742bd4e8123a7c078f0a8d9f3449fbfa8a320d7d90be641a2818db3c53d92c` and `f42db9774fa06e804ab7d596fc8b922a2b638921c418b87d0111151d290a6afe`; exactly one byte changes and old history remains. The agent is paused with zero active runs/errors. Both artifact work products have `isPrimary=false`, and descriptive titles fail a stricter title-helper assumption; these retained results are scoped editorial follow-up, not new merge gates. Six source-bound screenshots are uploaded and verified in the private primary QA report. - [Literal 9546 managed proof](https://d1p6rlowie26tp.cloudfront.net/runner-e2e/campaigns/gha-38485488621-1/index.html): original 19 assertions and completed judge pass, four native turns, child-bound240-byte file and session/workspace continuity. Checkout reports a verified generated target-lock mutation; full final porcelain was not retained. Signed execution-image identity remains separate from Core source. - Actual 651a Test deployment succeeds on one owned/pinned target. One ordinary Auto API-key Connect then fails native cleanup before hire. Controller turn/drain/suspend completion and service-recorded environment cleanup are observed; they do not certify physical deletion or native authority retirement. Failure/recovery/unknown holds are retained. No Legacy switch or unchanged paid retry. The two source repairs above require actual treatment. - [Current immutable Core preview](https://github.com/paperclipai/paperclip/actions/runs/38570365725) and matching DB/shared artifacts pass. One owned, pinned Test target serves exact `1c03`; identical migration history correctly skips the migrator. Ordinary Auto Codex Connect succeeds and hires native; saved native selection and QA bounds survive reload. The initial child preparation attempt fails before provider work, with actual stdout identifying `renewal_deadline`; its trigger remains unknown and the failure is retained. Normal Board **Try again** and **Resume** recover the child to Done, producing a browser-verified 44-byte file, SHA-256 `0a8458b1efcc2d7a0d815689458c4caab039a46c7c7a3e5805de6bc8b1a96ecc`. The actual parent callback reports the completed child document/file. The existing validator requires a parent-owned attachment, so recovery enters normal Review; after byte checking, normal **Approve completion** reaches parent Done. No forced status or duplicate parent file is used. The validator is unchanged from integrated and current master. Autonomous initial callback-to-Done is not proven. The same-child follow-up completes document revision 2 and publishes a second independently downloaded 44-byte file, SHA-256 `22022257300fae762784632d08d3bbe0bab61e2ce81f91864a14dcd7aa464591`; only the revision digit changes. The unchanged existing native-continuity and attachment oracles pass. All ten recorded runs are terminal: nine native successes and the retained pre-provider setup failure. The QA agent is paused with zero active runs. The pre-existing parent evidence scope mismatch is a separate follow-up, with ordinary completion review exercised rather than a forced status or relaxed validation. This unsigned Core preview remains distinct from post-merge private Cloud composition. ## Risks - Saved agents are not migrated. Explicit runner changes use normal configuration/session rules; historical runs retain their recorded execution. - Native readiness depends on verified assets and server-owned target qualification. A Legacy probe, HTTP200 or successful account save cannot prove native readiness. - Recovery exceptions remain restricted to validated completed-onboarding reports; process-loss, ownership and terminal-state safeguards remain active. Unexecuted live journeys stay open. - Linux ARM paid tasks, Windows, Alpine and 32-bit ARM remain deferred. Cold Cargo cache misses are recorded; no warm-cache speedup is claimed. - Historical invoices/physical cleanup remain unconfirmed and held. After merge, exact published npm canary, signed standard image/migrator, private composition and serving/live acceptance still require qualification. Production deployment/default promotion is not authorized. ## Model Used OpenAI Codex, GPT-6 family, with reasoning, tools, code execution and parallel agents. Exact serving snapshot and context-window size are not exposed. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used with available 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 linked public issues or PRs above - [x] I have not referenced internal/instance-local Paperclip issues or links - [x] My branch name describes the change and contains no internal ticket id - [x] I have run the stated focused tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation - [x] I have considered and documented risks - [x] All Paperclip CI gates are green on the current candidate - [x] Greptile is 5/5 with no open findings on the current candidate - [x] I will address all reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-14 11:33:02 -05:00
DottaandPaperclip	5da382fd59	feat(skills): require explicit merge modes (#10978) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Agents can select company skills and synchronize them to adapter runtimes > - The skill sync API replaced the complete selection without an explicit destructive choice > - Company package import also replaced conflicting skills by default > - These defaults could remove operator edits during setup and import reruns > - This pull request adds explicit assignment merge modes and safe package conflict handling > - The benefit is that reruns preserve operator work unless the caller explicitly requests replacement ## Linked Issues or Issue Description **What existing behavior does this improve?** This change improves agent skill synchronization and company package import. **Subsystem affected** This is a cross-cutting change across the shared contracts, server, CLI, and UI. **Current behavior** Agent skill synchronization replaces the full desired skill set from a modeless request. Package import replaces a conflicting skill when the caller does not select a conflict mode. **Proposed behavior** Agent skill synchronization requires `add`, `remove`, or `replace`. Package import skips conflicts by default. Each imported skill reports whether it was created, renamed, replaced, or skipped. **Reason and benefit** Setup and import reruns must preserve operator edits by default. Explicit destructive modes make data loss less likely and make each outcome inspectable. **Breaking changes** Callers of the agent skill sync API must now send `mode`. Callers that need the former behavior must send `replace`. Package import now uses `skip` when `onConflict` is absent. ## What Changed - Added required `add`, `remove`, and `replace` modes to the shared agent skill sync contract. - Added actionable `422` validation for missing or invalid modes. - Updated first-party UI and CLI callers with explicit modes. - Changed package skill conflict handling to use `skip` by default. - Kept plugin-owned and built-in stock skill imports on explicit `replace`. - Added created, renamed, replaced, and skipped results to company imports. - Added regression coverage for merge modes and package conflict outcomes. ## Verification - `pnpm check:token-gates` - `pnpm -r typecheck` - `pnpm build` - `pnpm test:run:serialized` (128 suites passed) - `pnpm --filter @paperclipai/skills-catalog test` (20 tests passed) - Focused agent skill route, company skill service, portability, CLI, and UI tests passed. - GitHub CI passed build, typecheck, canary, all general and serialized test shards, all browser shards, policy, security, and final verification on commit `2cfbb3e4c5`. - Greptile reviewed the latest commit at 5/5 with zero unresolved threads. ## Risks - This change intentionally rejects modeless agent skill sync requests. - The safe package default can leave an existing skill unchanged where the old default overwrote it. - All first-party callers now select a mode. Regression tests cover each outcome. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - OpenAI `gpt-5.6-sol` through Codex. The runtime used agentic reasoning, tool use, code execution, and repository editing. The runtime did not expose the 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 #` / `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>	2026-08-07 00:42:08 -05:00
Aron PrinsandDevin Foley	70b1a9109d	Improve CLI API parity coverage (#6626) ... ## Thinking Path > - Paperclip is a control plane for AI-agent companies, with the CLI acting as a scriptable operator and agent interface to that control plane. > - The REST API surface has grown across companies, agents, issues, routines, plugins, auth, workspaces, secrets, and operational inspection commands. > - The CLI had drifted from that API surface: some commands were missing, some command shapes differed from docs/reference material, and several edge cases only failed during end-to-end local-source testing. > - The local development runbook requires these tests to be disposable and isolated from a real `~/.paperclip`, `~/.codex`, or `~/.claude` installation. > - This pull request adds broad CLI/API parity coverage, fixes the actionable bugs found during that pass, and records the reproducible test log under `doc/logs`. > - The benefit is a more complete, scriptable CLI surface with regression coverage for the command families exercised by the parity run. ## What Changed - Added or expanded CLI command coverage for access/auth, companies, agents, projects, goals, issues and subresources, routines, plugins, workspaces, activity/run/cost/dashboard inspection, assets, skills, secrets, tokens, prompt/wake flows, and local setup helpers. - Fixed CLI/API parity bugs found during the run, including context profile patching, issue interaction optional payloads, malformed tree-hold errors, environment duplicate handling, configure invalid-section exit codes, worktree pnpm invocation, token agent ID resolution, plugin tool worker lookup, and routine webhook secret cleanup. - Added missing CLI wrappers and route coverage for health/access, invite resolution URL forwarding, join status normalization, secret lifecycle commands, LLM docs routes, available-skill isolation, positive board-claim coverage, and interactive `connect` prompt-flow tests. - Added a schema-backed `/api/openapi.json` route sufficient for CLI parity and `paperclipai openapi --json` smoke coverage. - Added `doc/logs/2026-05-24-cli-api-parity-e2e-log.md` with the detailed living test/bug log and renamed the log directory from `doc/bugs` to `doc/logs`. - Added `doc/plans/2026-05-23-cli-api-parity.md` and the OpenAPI parity reference used during the pass. OpenAPI note: this PR intentionally does not try to subsume `feature/openapi-spec`. The OpenAPI implementation here is schema-backed and better than the earlier route-inventory stub, but `feature/openapi-spec` is the fuller/better OpenAPI branch because it includes exact mounted-route coverage tests and additional current route coverage. That branch should stay as its own PR and can supersede this OpenAPI route implementation. ## Verification Targeted automated checks run: - `pnpm exec vitest run server/src/__tests__/openapi-routes.test.ts` - `pnpm exec vitest run server/src/__tests__/board-claim.test.ts` - `pnpm exec vitest run cli/src/__tests__/connect.test.ts` - `pnpm exec vitest run cli/src/__tests__/agent-lifecycle.test.ts` - `pnpm exec vitest run server/src/__tests__/plugin-database.test.ts` - `pnpm exec vitest run server/src/__tests__/routines-service.test.ts` - `pnpm --dir cli typecheck` - `pnpm --dir server typecheck` Manual/local E2E verification: - Ran the full disposable local-source CLI/API parity pass with isolated `PAPERCLIP_HOME`, `PAPERCLIP_CONFIG`, `PAPERCLIP_CONTEXT`, `PAPERCLIP_AUTH_STORE`, `CODEX_HOME`, and `CLAUDE_HOME` under `tmp/cli-api-parity`. - Verified `DATABASE_URL` and `DATABASE_MIGRATION_URL` stayed unset for the scratch server. - Verified live health and schema-backed OpenAPI responses on non-default port `3197`. - Revoked created board/agent tokens and cleaned up temporary plugins, secrets, non-default environments, and project workspaces. - See `doc/logs/2026-05-24-cli-api-parity-e2e-log.md` for the full command-by-command reproduction log. Not run: - Full `pnpm test`, `pnpm test:run`, or `pnpm build` were not run after the entire branch because the branch is broad and the parity pass used focused test/typecheck verification plus live isolated CLI reruns. ## Risks - This is a broad PR and touches many CLI command modules, so review surface is high. The changes are grouped around one theme, but a split may be easier if maintainers prefer narrower PRs. - The OpenAPI route in this PR is not the final/best OpenAPI implementation. `feature/openapi-spec` has stronger exact-route coverage and should remain the source for the dedicated OpenAPI PR. - The living log is intentionally detailed and large. It is useful for reproducibility but adds documentation weight. - No UI changes are intended; screenshots are not applicable. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - OpenAI Codex, GPT-5-based coding agent in Codex desktop. Exact served model/context-window identifier was not exposed in the local app. Work used shell/Git/GitHub CLI tooling, local source inspection, targeted test execution, and live isolated Paperclip CLI/API smoke testing. ## 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 run tests locally and they pass - [x] I have added or updated tests where applicable - [x] If this change affects the UI, I have included before/after screenshots - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Devin Foley <devin@devinfoley.com>	2026-06-02 17:13:29 -07:00