Use bounded partial directory pages with a global metadata limit and explicit listing/export warnings. Always inspect the configured entry directly so it remains readable beyond the first page.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
Stream initial personal files through bounded chunks into private staging and atomically publish without replacing an existing home. Keep the home-level runtime directory out of instruction enumeration and seeding while preserving nested user content.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - The server controls secrets, host files, outbound requests, and
workspace commands
> - A red-team review found cases where restricted callers could cross
these trust boundaries
> - These cases could expose credentials or let untrusted input reach
privileged resources
> - This pull request applies least-privilege checks at each affected
server boundary
> - The benefit is safer agent execution without changing the
private-instance bootstrap contract
## Linked Issues or Issue Description
**What happened?**
Several server paths used authorization, redaction, or content-delivery
rules that were too broad. Restricted agent keys could obtain
company-level operational data. Some adapter and instruction paths could
reach server-owned network or file resources without the required owner
approval.
**Expected behavior**
Paperclip must redact credential values, enforce restricted-key scopes,
guard outbound network access, prevent same-origin script execution, and
reserve host-level file and command controls for authorized operators.
**Steps to reproduce**
1. Configure an authenticated development instance at the parent commit.
2. Exercise the affected APIs with a restricted agent key or a
non-instance-admin company user.
3. Observe that the parent commit returns privileged data or accepts a
privileged operation.
4. Repeat on this branch and observe a redacted response, a safe
download, or an HTTP 403 response.
**Paperclip version or commit**
The findings reproduce from commit `39898ab22` and are fixed by this
pull request.
**Deployment mode**
Authenticated self-hosted server and local development modes.
**Installation method**
Built from source with pnpm.
## What Changed
- Redact generic secret `value` and `token` fields recursively in
structured logs.
- Classify exact and separator-suffixed `KEY` environment names as
secrets in company exports.
- Limit restricted self-identity responses and protect company run, log,
and secret catalog APIs.
- Route HTTP adapter requests through DNS-pinned SSRF protection with
exact private-origin allowlisting.
- Download HTML, SVG, and other script-capable assets with `nosniff` and
a sandbox CSP.
- Require instance-admin access for external instruction roots and
exports that read them.
- Block agent-authenticated host command persistence across supported
workspace runtime shapes.
- Apply the central runtime-management decision before workspace command
controls.
- Keep the documented first-user instance-admin claim contract
unchanged.
- Add regression tests and server-owner configuration documentation.
## Verification
- `pnpm -r typecheck` passes.
- The Node 24 remediation suite passes with 365 tests. It skips 25
environment-gated tests.
- `pnpm build` passes under Node 24.
- `git diff --check` passes.
- The full local runner reaches known macOS-only general-server harness
failures before the serialized route lane. The Linux PR matrix is the
authoritative full-suite gate.
## Risks
- Restricted agent keys now receive HTTP 403 responses from company-wide
run, log, and secret catalog endpoints.
- Script-capable assets now download instead of rendering inline.
- External instruction roots now require instance-admin access.
- Private HTTP adapter endpoints now require an exact origin in
`PAPERCLIP_HTTP_ADAPTER_PRIVATE_ENDPOINT_ALLOWLIST`.
- Public HTTP adapter endpoints remain enabled. Redirects and metadata
or link-local targets remain blocked.
- No database migration is required.
> 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. The exact serving snapshot and context-window size
are not exposed. The model used tool-enabled reasoning, repository
access, code execution, and 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
- [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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The runner package is useful only when the application can start,
observe, and recover a native Codex run safely.
> - Existing direct adapters must keep their current execution and
finalization paths.
> - The application boundary therefore needs additive persistence,
authorization, coordination, and recovery behind an explicit
experimental adapter.
> - This pull request adds that Codex-only boundary without activating
generalized providers, remote environments, or the later task/SDK
surfaces.
## Linked Issues or Issue Description
**Subsystem affected**
Shared contracts, database persistence, adapter utilities, server
native-runtime services, and the experimental Paperclip Runner adapter.
**Problem or motivation**
The already-landed runner package has a qualified Codex path, but the
application needs durable native-run state, guarded runtime selection,
authenticated coordination, tool security, finalization, and recovery
before the experimental adapter can be exercised safely.
**Proposed solution**
Add a Codex-only `paperclip_runner` application path behind the existing
default-off native-runner setting. Bind native state and coordination to
company/run identity, preserve persisted-run recovery, and leave every
direct adapter on its existing legacy execution path.
**Alternatives considered**
The earlier stack boundary introduced a generalized executor and
remote-environment lifecycle here. That made this PR depend on
implementations in higher PRs and changed reusable sandbox behavior
globally. Those pieces are now deferred together to #12592.
**Roadmap alignment**
ROADMAP.md does not list a conflicting native-runner integration
project. This change adds the application boundary for the existing
Runner architecture.
## What Changed
- Added native run/result/finalization/provider-trace persistence,
shared validators, and idempotent migration/replay coverage.
- Added guarded Codex-only runtime selection, authenticated PRP
coordination, recovery, finalization, and interaction services.
- Added run/company-bound tool-gateway authorization, credential
redaction, SSRF protections, and replay-safe behavior.
- Added the explicit `paperclip_runner` adapter behind the default-off
rollout setting.
- Preserved legacy answered-question wake projection and direct-adapter
execution/finalization paths.
- Hardened cancellation so only owned in-memory child processes are
signaled; persisted recycled PIDs/process groups are never trusted.
- Retained the narrow Claude ACPX isolated-context security follow-up
discovered after #12590.
- Deferred the generalized executor, provider ingress, remote lifecycle,
SDK/lab/eval work, release-process changes, and lockfile.
## Verification
- Changed-file delta against `master`: 133 files.
- GitHub Actions is the authoritative verification environment for this
PR.
- Full CI, security, and Greptile review will run on this lowest
unmerged stack PR.
- Local tests/build/typecheck were not run because this checkout is
resource constrained.
- Static diff/reference checks pass, and `pnpm-lock.yaml` is unchanged.
## Risks
- This touches central heartbeat and agent-route code, so legacy
compatibility is the primary risk.
- Runtime selection remains Codex-only and explicit; direct Codex,
Claude, OpenCode, process, HTTP, and plugin adapters remain on their
existing paths.
- Fresh native starts fail closed while the rollout flag is off;
persisted native records remain readable and recoverable.
- Cancellation, company/run binding, tool calls, status decisions, and
completion writes are guarded or replay-safe.
> 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.
## Model Used
OpenAI Codex, GPT-5.6, with repository tools, code execution, and
parallel agent review.
## 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 linked existing issues or described the issue in-PR
following the relevant issue template
- [x] I have not referenced internal or instance-local Paperclip issues
or links
- [x] My branch name describes the change and contains no internal
Paperclip ticket id
- [ ] I have run tests locally and they pass — GitHub Actions is
authoritative for this resource-constrained checkout
- [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 risks above
- [ ] All Paperclip CI and security gates are green
- [ ] Greptile is 5/5 with no open actionable findings
- [x] I will address all Greptile and reviewer comments before merge
## Stack
- Position: 3 of 5 overall; lowest of 3 currently unmerged
- Base: `master`
- Previous:
[#12590](https://github.com/paperclipai/paperclip/pull/12590), qualified
Claude ACPX runtime — merged
- Next: [#12592](https://github.com/paperclipai/paperclip/pull/12592),
generalized Codex executor, task experience, and developer SDKs
---------
Co-authored-by: Dev Agent <dev@paperclip.ing>
Add @deprecated JSDoc and inline comments to bootstrapPromptTemplate
references in agent-instructions and company-portability services.
This field is superseded by the managed instructions bundle system.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
Keep existing instructionsFilePath agents in external-bundle mode during edits, expose legacy promptTemplate as a deprecated virtual file, and reuse the shared PackageFileTree component in the Prompts view.
Co-Authored-By: Paperclip <noreply@paperclip.ing>
