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Author SHA1 Message Date
Harshit Khemani c297ba2a80 fix(codex-local): replace stale auth.json copy with symlink on prepare (#5028) (#5240) 
## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - codex_local runs Codex CLI under a per-company "managed home" so
multiple companies don't trample on each other's session state
> - For `auth.json` specifically, the managed home keeps a SYMLINK to
the user's real `~/.codex/auth.json` rather than a copy — Codex refresh
tokens rotate and are single-use, so any copy goes stale the moment the
source rotates and every subsequent run dies with `401
refresh_token_reused`
> - Older Paperclip versions copied `auth.json` instead. After
upgrading, `ensureSymlink()` saw a regular file at the target, hit `if
(!existing.isSymbolicLink()) return;`, and silently kept the stale copy
> - This pull request makes the upgrade path self-healing inside
`ensureSymlink()` itself: when the target is a regular file, unlink it
and create the symlink, since the target lives under the
Paperclip-managed home and is safe to delete. Directories are skipped to
avoid `EISDIR` on Unix (and inconsistent behavior on Windows)
> - The benefit is operators who upgraded from a copy-based version stop
getting refresh-token-reused failures without having to manually purge
`companies/<id>/codex-home/auth.json`, and the healing is
defense-in-depth even outside the `prepareManagedCodexHome` cleanup path

## What Changed

- `packages/adapters/codex-local/src/server/codex-home.ts` —
`ensureSymlink()` previously bailed out of the
`!existing.isSymbolicLink()` branch, leaving any pre-existing regular
file untouched. Now unlinks and recreates the symlink in that branch via
the existing `createExpectedSymlink()` helper (preserves the EEXIST
race-tolerance behavior added in #5119). A guard skips directories so
the call never throws `EISDIR` and aborts `prepareManagedCodexHome`.
Inline comment explains the safety: target is always under the
company-scoped managed home
(`<paperclipHome>/instances/<id>/companies/<companyId>/codex-home/`),
never the user's real `~/.codex`.
- `packages/adapters/codex-local/src/server/codex-home.test.ts` — adds a
regression test for #5028: pre-seed a stale copy at the target, run
`prepareManagedCodexHome`, assert the target is now a symlink and reads
through to the fresh source. The existing concurrent-symlink test is
preserved.

## Verification

```
pnpm --filter @paperclipai/adapter-codex-local exec vitest run
# Test Files  8 passed (8)
# Tests       26 passed (26)
pnpm --filter @paperclipai/adapter-codex-local exec tsc --noEmit
# clean
```

Manual repro flow that the regression test mirrors:
1. Create a stale copy: `echo '{"token":"old"}' >
<managedHome>/auth.json`.
2. Rotate source: `echo '{"token":"new"}' > ~/.codex/auth.json`.
3. Trigger any codex_local run — `prepareManagedCodexHome` is called
from the execute path, the managed file is now a symlink to the source,
and the CLI sees the fresh token.

## Risks

- **Low risk.** The new branch only fires when the target file is a
regular file (the upgrade path) — a pure copy that Codex couldn't have
written, since Codex never writes into the managed home. Operators in
steady-state on the symlink-based version are unaffected.
- The `fs.unlink` only runs against the per-company managed-home path,
never the user's real `~/.codex`. Inline comment makes this guarantee
explicit.
- A directory at the auth.json path is left in place (no silent `EISDIR`
crash) — this requires operator inspection rather than autonomous
deletion.
- The healing uses `createExpectedSymlink()` so it remains tolerant of
EEXIST races with concurrent prepare calls (the concurrent-symlink test
still passes).
- No DB / migration / schema impact.

## Model Used

- Anthropic Claude Opus 4.7 (claude-opus-4-7), via Claude Code CLI with
extended tool use (Read / Edit / Bash / Grep). No extended-thinking
budget consumed beyond default.

## 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
- [ ] If this change affects the UI, I have included before/after
screenshots — N/A, adapter-only
- [x] I have updated relevant documentation to reflect my changes —
inline comment explains the why and the safety of the unlink
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
- [x] I searched the GitHub PR list for similar PRs and confirmed this
is not a duplicate

Fixes #5028.

---------

Co-authored-by: Devin Foley <devin@paperclip.ing>
Co-authored-by: Paperclip <noreply@paperclip.ing>
 2026-06-10 06:50:20 -07:00
Dotta 38c185fb8b [codex] Add agent permissions and controls plan (#6386) 
## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies by keeping
task ownership, approvals, and operator control inside one control
plane.
> - Agent permissions and plugin-hosted company settings sit on the
boundary between autonomy and governance.
> - V1 needs scoped task assignment rules, plugin extension points, and
clearer company access surfaces without weakening company boundaries.
> - The branch builds the core authorization service, plugin SDK/host
APIs, and UI simplifications needed to support those controls.
> - Paperclip EE plugin surfaces were intentionally moved out of this
core PR per review direction, so this PR now carries only the public
core/plugin infrastructure work.
> - The latest updates preserve the PAP-9937 branch changes that belong
in this PR, remove the `design/` artifacts, and exclude the experimental
`plugin-briefs` package.
> - Greptile feedback was applied through the authorization/audit paths
and the final cleanup commit was re-reviewed at 5/5 with no unresolved
Greptile threads.
> - The benefit is safer assignment control with extension hooks for
richer permission products while preserving simple defaults for normal
operators.

## What Changed

- Added scoped task-assignment authorization decisions and routed
issue/agent assignment mutations through the authorization service.
- Added plugin SDK and host APIs for company settings slots,
authorization policy/grant management, assignment previews, and bridge
invocation scope propagation.
- Simplified core company access UI and moved advanced controls behind
plugin-provided settings surfaces.
- Added retry-now affordances for blocked issue next-step notices.
- Added protected-assignment enforcement for persisted
agent/project/issue policies, including explicit-grant fallback
behavior.
- Added incremental principal-access compatibility backfill for active
agent memberships and role-default human permission grants.
- Added the Markdown code block wrap action fix from the latest branch
changes.
- Removed `design/` artifacts from the PR and removed
`packages/plugins/plugin-briefs` from the final diff.
- Addressed Greptile feedback for plugin actor sanitization, legacy
membership handling, audit pagination, unknown grant-scope metadata, and
startup test mocks.

## Verification

- `pnpm exec vitest run server/src/__tests__/access-service.test.ts
server/src/__tests__/company-portability.test.ts` -> 2 files passed, 54
tests passed.
- `pnpm exec vitest run
server/src/__tests__/server-startup-feedback-export.test.ts
server/src/__tests__/access-service.test.ts
server/src/__tests__/company-portability.test.ts` -> 3 files passed, 62
tests passed.
- `pnpm exec vitest run
server/src/__tests__/authorization-service.test.ts
server/src/__tests__/plugin-access-authorization-host-services.test.ts
server/src/__tests__/server-startup-feedback-export.test.ts` -> 3 files
passed, 28 tests passed.
- `pnpm --filter @paperclipai/server typecheck` -> passed.
- `git diff --check` -> passed.
- `node ./scripts/check-docker-deps-stage.mjs` -> passed.
- `CI=true pnpm install --frozen-lockfile --ignore-scripts` -> passed
with no lockfile update.
- `pnpm exec vitest run
ui/src/components/MarkdownBody.interaction.test.tsx` -> 1 test passed.
- `git ls-files design packages/plugins/plugin-briefs | wc -l` -> 0.
- GitHub CI on `40cd83b53` -> all checks passed, merge state `CLEAN`.
- Greptile on `40cd83b53` -> 5/5, 102 files reviewed, 0
comments/annotations added, 0 unresolved review threads.
- Confirmed the PR diff contains no `design/`,
`packages/plugins/plugin-briefs`, `pnpm-lock.yaml`, or
`.github/workflows` changes.

## Risks

- Medium: task assignment authorization paths are behaviorally stricter
for protected/private policy data, so existing plugin-authored policies
may block assignment until explicit grants or approval flows are
configured.
- Medium: plugin-host authorization APIs expand the surface area
available to trusted plugins and need careful review for company
scoping.
- Low: startup now performs a principal-access compatibility backfill,
but the migration and runtime backfill use conflict-tolerant inserts.

> 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 coding agent, tool-enabled workflow with shell,
git, and GitHub CLI access.

## 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: Paperclip <noreply@paperclip.ing>
 2026-05-22 08:12:52 -05:00
Dotta 0096b56a1c [codex] Add LLM Wiki plugin host support (#5597) 
## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies.
> - The plugin system needs host contracts and runtime support before
large plugins can integrate cleanly.
> - The source branch mixed the LLM Wiki package with supporting
host/runtime work, managed plugin skills, root-level storage spaces, and
a bookmarks reference plugin.
> - [PAP-9173](/PAP/issues/PAP-9173) asked for the current branch to be
split by file boundary: plugin package separately from everything else.
> - [PAP-9188](/PAP/issues/PAP-9188) clarified that LLM Wiki may have
plugin-local spaces, but Paperclip core should not reorganize top-level
local storage into spaces.
> - Follow-up review clarified that the bookmarks example should not
ship in this PR either.
> - This pull request contains the
non-`packages/plugins/plugin-llm-wiki/` host/runtime work, keeps runtime
state under the selected Paperclip instance root, and no longer includes
the bookmarks example.

## What Changed

- Added/updated plugin host contracts, SDK types, worker RPC plumbing,
managed plugin skill support, and related server tests.
- Removed the bookmarks example plugin package and its
bundled-example/workspace references.
- Removed the root-level local spaces CLI/migration surface and restored
instance-root runtime defaults for config, db, logs, storage, secrets,
workspaces, projects, and adapter homes.
- Replaced shared root `space-paths` helpers with `home-paths` helpers
for core runtime storage.
- Tightened stranded recovery unique-conflict detection so concurrent
recovery scans reuse the raced recovery issue when Postgres errors are
wrapped.
- Kept `packages/plugins/plugin-llm-wiki/` out of this PR diff;
plugin-local spaces remain in the stacked plugin-only PR.

## Verification

- `pnpm exec vitest run cli/src/__tests__/data-dir.test.ts
cli/src/__tests__/home-paths.test.ts cli/src/__tests__/onboard.test.ts
packages/shared/src/home-paths.test.ts
packages/db/src/runtime-config.test.ts
server/src/__tests__/agent-instructions-service.test.ts
server/src/__tests__/claude-local-execute.test.ts
server/src/__tests__/codex-local-execute.test.ts`
- `pnpm exec vitest run packages/db/src/runtime-config.test.ts`
- `pnpm exec vitest run
server/src/__tests__/plugin-routes-authz.test.ts`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm exec vitest run
server/src/__tests__/heartbeat-process-recovery.test.ts -t "reuses the
raced stranded recovery issue"` skipped locally because embedded
Postgres did not initialize on this macOS temp host; the code path was
typechecked and is covered by Linux CI.
- Boundary check: no core references remain for `PAPERCLIP_SPACE_ID`,
`spaces migrate-default`, `@paperclipai/shared/space-paths`,
`registerSpacesCommands`, or the removed bookmarks example.
- Previous PR head `4f23e034` had green GitHub checks: `verify`, all
four serialized server shards, `e2e`, `Canary Dry Run`, `policy`, Snyk,
and `Greptile Review`. Current head `582f466d` is re-running checks
after the bookmarks deletion.

## Risks

- Plugin host changes touch shared runtime paths, so regressions would
most likely appear in adapter startup, plugin loading, or local dev path
defaults.
- Removing the bookmarks example also removes one demonstration of
plugin database namespaces plus local-folder persistence; remaining
plugin examples still cover bundled example discovery and plugin host
flows.
- The plugin package itself is intentionally deferred to the stacked
plugin-only PR, where LLM Wiki plugin-local spaces live.
- Existing installs that tested the transient root-level spaces CLI
should stop using it; this PR intentionally removes that unsupported
migration surface before merge.

> 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 Codex via Codex CLI, tool use and local code execution
enabled; context window 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 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, except where noted above
for host-specific embedded Postgres initialization
- [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

Stacked follow-up: PR #5592 contains only
`packages/plugins/plugin-llm-wiki/` and targets this branch.

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
 2026-05-10 07:34:12 -05:00
Devin Foley 9042b8d042 Write apikey-mode auth.json so Codex CLI 0.122+ can authenticate via OPENAI_API_KEY (#5276) 
## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - The Codex adapter spawns the OpenAI Codex CLI to drive the model
> - Codex CLI 0.122 changed how it reads credentials: it ignores
`OPENAI_API_KEY` from the environment and reads only
`$CODEX_HOME/auth.json`
> - Without auth.json, Codex 0.122+ returns 401 "Missing bearer or basic
authentication" on `/v1/responses` even when `OPENAI_API_KEY` is
forwarded into the sandbox or remote shell
> - This pull request materializes an apikey-mode `auth.json` in the
managed Codex home (or per-run for the test probe) when an
`OPENAI_API_KEY` is configured
> - The benefit is configured Codex API keys authenticate correctly with
current Codex CLI versions across local, SSH, and sandbox targets

## What Changed

- `codex-home.ts`: add `writeApiKeyAuthJson()` and let
`prepareManagedCodexHome` accept an `apiKey` override that replaces the
symlinked host auth.json with an apikey-mode file
- `execute.ts`: pass `envConfig.OPENAI_API_KEY` into
`prepareManagedCodexHome` so the managed (and synced-to-remote) Codex
home authenticates via the configured key
- `test.ts`: when `OPENAI_API_KEY` is available, wrap the hello probe
with a small shell that materializes a per-run `$CODEX_HOME/auth.json`
before exec'ing codex; key content rides through env to avoid leaking
into process listings
- Update the `codex_hello_probe_auth_required` hint to explain Codex CLI
does not read `OPENAI_API_KEY` from env

## Verification

- `pnpm vitest run --no-coverage --project
@paperclipai/adapter-codex-local`
- `pnpm typecheck` clean
- Manual: Codex 0.122.0 with empty `CODEX_HOME` returns 401 with
env-only auth; with this change it authenticates cleanly

## Risks

Low risk — when no API key is configured, behavior is unchanged (no
auth.json written, existing chatgpt-mode flow preserved). Apikey-mode
`auth.json` is the upstream-supported format.

## Model Used

Claude Opus 4.7 (1M context)

## 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 — N/A (no UI)
- [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
 2026-05-05 08:00:27 -07:00
dotta d53714a145 fix: manage codex home per company by default 2026-03-20 14:44:27 -05:00
dotta 3b03ac1734 Scope Codex local skills home by company 2026-03-18 14:38:39 -05:00
Dotta bb788d8360 Treat Codex bootstrap logs as stdout 
Co-Authored-By: Paperclip <noreply@paperclip.ing>
 2026-03-16 18:26:36 -05:00
Dotta a393db78b4 fix: address greptile follow-up 
Co-Authored-By: Paperclip <noreply@paperclip.ing>
 2026-03-13 14:53:30 -05:00
Dotta 528505a04a fix: isolate codex home in worktrees 2026-03-13 11:53:56 -05:00