## Thinking Path
> - Paperclip is the control plane for companies that use AI agents.
> - Apps give humans and agents controlled access to external services.
> - The existing app detail flow split permissions, tests, setup, and
activity across separate pages.
> - The split made access rules harder to understand and made reconnect
work hard to find.
> - New write actions also defaulted to Ask first, which did not match
the intended connection policy.
> - This pull request combines permission control and action testing,
removes the setup page, and moves connection activity into Audit.
> - The benefit is one clear place to configure, test, reconnect, and
review each app.
## Linked Issues or Issue Description
**What existing behavior does this improve?**
The installed app Permissions, Test, Setup, and Activity views.
**Subsystem affected**
Cross-cutting. This change updates the React UI, shared app defaults,
server permission behavior, tests, smoke scripts, and connection
documentation.
**Current behavior**
App access and action testing use separate pages. The app detail view
also links to a setup page after installation. Connection activity uses
a separate tab. New write actions default to Ask first.
**Proposed behavior**
Permissions uses the connection access language from the initial flow.
It includes searchable Read and Write sections, a three-state permission
control, and a Test dialog for each action. Reconnect appears below a
Needs attention header on Permissions and Review. Old Setup and Test
links redirect to Permissions. Old Activity links redirect to the
filtered company Audit feed. New write actions default to Allowed.
**Reason and benefit**
A person can understand and test app access without moving between
several pages. Reconnect work stays visible where the person reviews the
connection. Audit events use one consistent feed and filter model. New
connections have the intended default policy.
**Breaking changes**
The Setup, Test, and app Activity tabs are removed. Existing deep links
redirect to their replacement pages. Existing saved action permissions
do not change. Only defaults for new write actions change.
**Additional context**
This builds on the managed app connection work in #12728. A search found
no duplicate open pull request or issue.
## What Changed
- Combined action testing with Permissions.
- Added searchable Read and Write action groups.
- Added Off, Ask first, and Allowed controls with tooltips.
- Added an action Test dialog with agent selection, arguments, and
formatted results.
- Removed the installed-app Setup and Activity tabs.
- Added reconnect guidance to Permissions and Review when a connection
needs attention.
- Routed connection activity into the company Audit feed and preserved
the Apps & tools filter in streamlined Audit.
- Moved connection removal to the Connectors-page management menu.
- Made new write actions default to Allowed across connection creation
paths.
- Updated regression tests, browser suites, smoke scripts, and
connection documentation.
## Verification
- `pnpm check:token-gates`
- `pnpm exec vitest run packages/shared/src/app-definitions.test.ts
server/src/__tests__/generic-mcp-connection.test.ts
server/src/__tests__/tool-access-service.test.ts
ui/src/components/AppConnectionSidebar.test.tsx
ui/src/pages/apps/AppDetail.test.tsx
ui/src/pages/apps/AppNotConnected.test.tsx
ui/src/pages/apps/AppsConnect.test.tsx ui/src/pages/apps/Browse.test.tsx
ui/src/pages/apps/Connections.test.tsx
ui/src/pages/apps/composio-services.test.ts
ui/src/pages/audit/AuditFeed.test.tsx
ui/src/pages/tools/PasteConfigTab.test.tsx` (517 tests passed)
- `pnpm exec vitest run ui/src/pages/apps/app-detail/TestPanel.test.tsx
ui/src/pages/audit/AuditHub.test.tsx
ui/src/pages/audit/AuditFeed.test.tsx
ui/src/pages/apps/AppDetail.test.tsx ui/src/pages/apps/Browse.test.tsx`
(96 tests passed)
- Targeted Playwright verification for connection removal, rename on
Permissions, inline action testing, and Smoke Lab Audit evidence (5
flows passed)
- `pnpm -r typecheck`
- `pnpm build`
- `pnpm test:run` completed with 5,755 passing tests and 20 unrelated
macOS harness failures. The failures use `/tmp` versus `/private/tmp`,
invalid ports above 65535, and workspace fixtures outside this change.
## Risks
- Low migration risk. This change has no database migration.
- Old app-detail URLs depend on redirect compatibility.
- New connections grant write actions by default. Finalization remains
configure-authorized and audited, Ask first and Off remain available per
action, and existing connections keep their saved policy.
> 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, exact model ID `gpt-5`. The client does not expose the
context-window size. The model used reasoning, repository tools, code
execution, and browser verification.
## 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 Apps subsystem gives humans and agents governed access to
external tools.
> - The current connection flow hides Apps behind an experimental gate
and repeats setup text.
> - Google sharing choices and generic MCP permissions do not use one
consistent opening model.
> - Self-hosted installs also need a safe default origin for managed
OAuth without a manual config file.
> - This pull request makes Apps available, simplifies connection setup,
and applies one governed permissions model.
> - The benefit is a shorter connection flow that works on a clean
self-hosted install.
## Linked Issues or Issue Description
**What existing behavior does this improve?**
This improves the Apps connection setup flow, managed Google connection
flow, generic MCP connection flow, navigation, and runtime origin
discovery.
**Subsystem affected**
Cross-cutting. This changes `ui/`, `server/`, `packages/shared/`,
connector documentation, and browser tests.
**Current behavior**
Apps require an experimental switch. Setup pages repeat titles and
explanatory copy. Connection names require manual input. Google
credential sharing does not always offer both personal and organization
access. Generic MCP providers do not start with the same permission
choices. Managed OAuth needs a public URL setting even when the request
already has a safe HTTPS origin.
**Proposed behavior**
Apps are available by default. Setup asks only for required permissions
and sharing choices. Paperclip creates conflict-free connection names.
Google apps and generic MCP providers use the same human and agent
access model. Managed OAuth derives a validated same-origin HTTPS URL
when no explicit public URL is set.
**Reason and benefit**
A clean self-hosted install can connect a managed Google app without
hidden setup. Humans can share a service account with their
organization. The shorter flow reduces duplicated choices and setup
errors.
**Breaking changes**
The Apps experimental switch is removed. Existing connection APIs remain
compatible. New connections can receive a numeric suffix when a name
already exists.
No duplicate or related public issue was found.
## What Changed
- Removed the Apps experimental gate and the breadcrumb that leaves the
Apps section.
- Simplified all connection setup pages and moved optional provider
requirements into one small link.
- Added consistent human and agent access choices for Google apps,
Zapier, and generic MCP connections.
- Added organization sharing to Google Workspace credentials while
keeping personal access available.
- Generated connection names automatically and resolved name conflicts
with numeric suffixes.
- Derived a validated public HTTPS origin from the request for
config-free managed OAuth.
- Updated connector contracts, tests, browser coverage, and authoring
documentation.
## Verification
- `pnpm check:token-gates`
- `pnpm -r typecheck`
- `pnpm build`
- `pnpm exec vitest run server/src/__tests__/tool-access-service.test.ts
server/src/__tests__/generic-mcp-connection.test.ts` (273 passed)
- Targeted UI/service regression suite (308 passed)
- Six targeted Playwright connection journeys on a fresh onboarding
instance (6 passed)
- Fresh-install browser proof through Tailscale HTTPS: enrolled with
Paperclip Cloud, connected managed Google Drive, and completed a real
read operation.
- [Exact-head CI
run](https://github.com/paperclipai/paperclip/actions/runs/33669760711):
all 23 matrix jobs passed, including build, typecheck, server,
serialized, canary, and all browser shards.
- Greptile 5/5 on `0ae2a859f269984ee950d0af231a5b09a06f3dfd`, with no
unresolved review threads.
## Risks
Apps are now visible to all operators. The removed experimental flag no
longer hides unfinished app definitions. Managed Google availability
still depends on the Cloud profile rollout and active instance
enrollment. Automatic conflict handling changes only the display name of
a newly conflicting connection.
> I checked [`ROADMAP.md`](ROADMAP.md). MCP Tool Gateway and Apps are
shipped. Connected Apps is planned, and this change improves the
existing shipped connection flow.
## Model Used
OpenAI Codex, GPT-5, with reasoning, browser control, tool use, and code
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 backend now turns agent requests into durable connection
intents.
> - Operators need a clear path to inspect, configure, and finish those
requests.
> - The experience must preserve identity, agent access, and interrupted
setup state.
> - This pull request adds the connection intent setup experience across
the app UI.
> - The benefit is one guided flow from agent request to governed
connection.
## Linked Issues or Issue Description
Refs #11965
This is stack 9 of 11. It depends on stack 8 and replaces another
reviewable part of #11965.
## What Changed
- Add connection intent cards and setup flow integration.
- Add browse, connection, app detail, and sidebar experience updates.
- Preserve exact draft identity and access choices across resume and
OAuth recovery.
- Add focused UI, architecture, policy, and end-to-end coverage.
- Keep transient retained-connection lookup failures retryable instead
of misclassifying them as missing targets.
- Align the dark-mode E2E contract with the intentionally hidden
Gateways and Profiles sidebar tabs.
## Verification
- `pnpm -r typecheck`
- Focused UI result: 372 tests passed across 20 files.
- AppsConnect regression suite: 80/80 passed, including failed
connection and application lookups during retained reconnect.
- `pnpm --filter @paperclipai/ui exec vitest run
src/components/AppsSidebar.test.tsx` (1 passed)
- `pnpm check:token-gates`
- `pnpm --filter @paperclipai/db check:migrations`
- `pnpm build`
## Risks
- An interrupted OAuth flow can leave a durable draft that needs resume.
- The UI resumes the exact draft and keeps its identity and agent access
settings.
- Retained reconnect retries refetch connections and applications
together to avoid mixing partial snapshots.
- Gateways and Profiles remain route-accessible but intentionally absent
from the sidebar until their existing ship gate is lifted.
- The change does not add a database migration.
> I checked `ROADMAP.md`. This stack continues the existing app
connection work from #11965 and does not duplicate another planned item.
## Model Used
OpenAI Codex, GPT-5. The runtime model ID and context window were not
exposed. The model used reasoning, tool use, and code 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 linked the public source pull request with `Refs #`
- [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 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.
> - External tools need explicit identity and access boundaries.
> - Shared connection credentials cannot represent every user-scoped use
case.
> - Grants must stay company-scoped and support safe delegation.
> - This pull request adds connection grants, identity rules, and their
database contract.
> - The benefit is durable control over which identity an agent may use.
## Linked Issues or Issue Description
Refs #11965
This is stack 3 of 11. It depends on stack 2 and replaces another
reviewable part of #11965.
## What Changed
- Add company and user connection grants.
- Add delegated identity and membership rules.
- Synchronize database, shared, server, and UI contracts.
- Register the grant-member replacement route in the OpenAPI surface in
the same layer that mounts it.
- Add migration 0231 with replay-safe guards and coverage.
## Verification
- `pnpm -r typecheck`
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/tool-access-service.test.ts`
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/openapi-routes.test.ts` (5 passed)
- `pnpm --filter @paperclipai/db check:migrations`
- `pnpm build`
## Risks
- Incorrect grant selection could expose the wrong credential scope.
- The service enforces company and subject boundaries before credential
use.
- Migration 0231 is generated, ordered after 0230, and safe to replay.
> I checked `ROADMAP.md`. This stack continues the existing app
connection work from #11965 and does not duplicate another planned item.
## Model Used
OpenAI Codex, GPT-5. The runtime model ID and context window were not
exposed. The model used reasoning, tool use, and code 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 linked a public issue or pull request with `Refs #`
- [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 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.
> - App connections must work in both the operator UI and agent tool
gateway.
> - The first stack layer adds secure remote connections.
> - Operators still need clear setup, test, and recovery states.
> - This pull request adds the gateway behavior and the workspace
connection experience.
> - The benefit is a connection flow that is easier to understand and
recover.
## Linked Issues or Issue Description
Refs #11965
This is stack 2 of 11. It depends on stack 1 and replaces another
reviewable part of #11965.
## What Changed
- Improve remote tool gateway connection behavior.
- Add clearer app setup, test, and recovery states.
- Add focused server and UI tests for the new paths.
- Keep the diff isolated from later identity and catalog work.
- Stabilize DNS-pinned remote HTTP protocol fixtures and the
managed-runtime public-origin fixture for this independently tested
layer.
## Verification
- `pnpm -r typecheck`
- `pnpm --filter @paperclipai/server exec vitest run
src/__tests__/tool-access-service.test.ts` (150 passed)
- `pnpm test:run`
- `pnpm check:token-gates`
- `pnpm build`
## Risks
- Gateway errors now surface through new user-facing states.
- A stale connection can require a new setup attempt.
- The change does not add a database migration.
- The injected HTTP transport and public URL are test-only fixtures;
production DNS pinning and runtime behavior are unchanged.
> I checked `ROADMAP.md`. This stack continues the existing app
connection work from #11965 and does not duplicate another planned item.
## Model Used
OpenAI Codex, GPT-5. The runtime model ID and context window were not
exposed. The model used reasoning, tool use, and code 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
- [x] My branch name describes the change 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 Apps subsystem connects company tools through governed provider
connections.
> - A company can need more than one account for the same provider.
> - The current database constraint and Apps flow assume one named
connection per company.
> - New quarantined actions also need an explicit review decision before
activation.
> - This pull request supports multiple provider connections and
complete action review decisions.
> - The benefit is safer access control and a clear multi-account Apps
workflow.
## Linked Issues or Issue Description
Refs: #11040
**Subsystem affected**
Cross-cutting. This change affects the Apps UI, the tool access API, the
shared request contract, and the database schema.
**Problem or motivation**
The connection name constraint prevents a company from keeping more than
one connection for a provider. The Apps UI also reuses an existing OAuth
connection when a user asks to connect another account. Action review
can enable selected entries without recording a decision for every
quarantined action.
**Proposed solution**
Remove the company and connection name uniqueness constraint. Let users
open, count, edit, and create multiple provider connections. Require the
finish request to cover every quarantined action exactly once before the
server activates reviewed entries.
**Alternatives considered**
The UI could generate unique internal names and keep the database
constraint. This would preserve a one-connection assumption in the data
model and would make display names part of identity. The server could
also infer review decisions from enabled actions. This would not
distinguish a reviewed disabled action from an action that the user did
not review.
**Roadmap alignment**
This change extends the completed MCP Tool Gateway and Apps milestone.
It also supports the Connected Apps roadmap item. It follows the
navigation and connection management work in #11040.
## What Changed
- Remove the company-scoped connection name uniqueness index with an
ordered and idempotent migration.
- Add a reviewed action list to the finish-app contract and reject
incomplete or duplicate review decisions.
- Activate reviewed entries and keep unreviewed quarantined entries
blocked.
- Enable a completed connection and preserve the company and connection
scope in all updates.
- Show provider connection counts and open the provider setup page from
Browse.
- Let users edit existing connections or connect another account without
reusing an active OAuth connection.
- Update focused server and UI coverage for multiple connections and
action review.
## Verification
- Ran the focused Apps UI suite. All 116 tests passed in 11 files.
- Ran the focused server and CLI suite. All 276 tests passed in 3 files.
- Ran `pnpm --filter @paperclipai/db check:migrations`. The migration
safety check passed.
- Ran `pnpm -r typecheck`. All projects passed.
- Ran `pnpm build`. All projects built successfully.
- Ran `pnpm test:run`. It passed 3,735 tests and skipped 4 tests. One
worktree-safety assertion failed because the execution workspace reloads
its worktree marker. The same test passed with an isolated non-worktree
marker.
- Ran `pnpm check:token-gates`. It reports 12 existing violations in the
unchanged `PaperclipOrbit3D.tsx` file from the target branch.
- Started the six affected Playwright specifications. Chromium could not
start because the host does not provide `libatk-1.0.so.0`. The GitHub
e2e jobs will verify these specifications.
- GitHub Actions passed every final-head CI gate, including all three
e2e shards and the aggregate `e2e` and `verify` jobs.
- Greptile reviewed final commit `9af9200426` at 5/5 with zero review
threads.
## Risks
- Removing the name uniqueness index permits duplicate display names.
Stable connection IDs and UIDs remain unique within a company.
- The finish-app endpoint accepts the new review field as optional for
backward compatibility. When clients send it, the server requires a
complete decision for all quarantined actions.
- Multiple OAuth connections depend on the explicit new-connection route
flag. Focused tests cover active and draft connection reuse.
- The migration is ordered after migration 0210. Its `DROP INDEX IF
EXISTS` statement is safe to repeat.
> 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 with the `gpt-5.6-sol` model assisted this change. The
agent used repository tools, code execution, test execution, and agentic
reasoning. The Codex runtime manages the context window.
## 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 Apps UI manages app discovery and app connections.
> - The managed worktree runtime starts agent work in repository
worktrees.
> - The Apps routes do not match the main discovery flow, and the
connections view lacks a delete action.
> - Legacy managed worktrees can also start before their pending seed
operation runs.
> - This pull request makes app discovery the main Apps route and makes
connection management explicit.
> - It also seeds legacy managed worktrees before runtime startup and
makes the CLI read the repository-local config.
> - The benefit is a clearer Apps workflow and a safer managed-worktree
startup path.
## Linked Issues or Issue Description
**What existing behavior does this improve?**
This improves the Apps navigation, app connection management, managed
git-worktree startup, and CLI worktree selection.
**Subsystem affected**
Cross-cutting. The change affects `ui/`, `server/`, `cli/`, and
development documentation.
**Current behavior**
The `/apps` route opens the connections list while discovery uses a
nested route. The connections list has no delete action. Some legacy
managed worktrees can start runtime work before their pending seed
operation runs. The CLI can also read an ambient Paperclip config
instead of the repository-local config.
**Proposed behavior**
The `/apps` route opens Browse, and `/apps/connections` opens the
connection list. Users can delete a connection after confirmation.
Runtime startup seeds legacy managed worktrees when required. The CLI
resolves the current worktree from the repository-local
`.paperclip/config.json` file.
**Reason and benefit**
Users can discover apps from the canonical Apps route and can manage
existing connections from a dedicated route. Legacy worktrees receive
their required repository content before agent runtime starts. CLI
worktree selection stays scoped to the current repository.
**Breaking changes**
The `/apps` and `/apps/browse` route behavior changes. Old Browse links
redirect to `/apps`. The change does not modify an API schema or
database schema.
## What Changed
- Make Browse the canonical `/apps` page and move the connection list to
`/apps/connections`.
- Align Apps navigation, redirects, attention links, empty states, and
connection actions with the new routes.
- Add connection deletion with confirmation and clear failure feedback.
- Seed legacy managed git worktrees before runtime startup when their
seed status is pending.
- Read the CLI worktree selection from the repository-local Paperclip
config.
- Update focused UI, server, CLI, and development documentation
coverage.
## Verification
- Ran 202 focused UI, server, and CLI tests. All tests passed.
- Ran `pnpm -r typecheck`. All projects passed.
- Ran `pnpm build`. All projects built successfully.
- Ran `pnpm test:run`. The server and UI stages passed 7,168 tests. The
CLI stage found one environment-sensitive secrets test because this
workspace injects static AWS credentials. The isolated CLI file passed
all 8 tests after those injected variables were unset.
- Ran `pnpm check:token-gates`. It reports 12 existing color-token
violations in the unchanged `PaperclipOrbit3D.tsx` file from the target
branch. This pull request does not modify that file.
- Ran focused regression coverage for repository-root CLI config
resolution and connection deletion state. All tests and affected package
typechecks passed.
- Collected all 27 tests in the six changed Playwright specifications
successfully.
- GitHub Actions passed every latest-head CI gate, including all three
e2e shards and the aggregate `e2e` and `verify` jobs.
- Greptile reviewed the final commit at 5/5 with zero unresolved
threads.
## Risks
- Existing bookmarks for `/apps/browse` redirect to `/apps`.
- Connection deletion changes visible connection state and requires user
confirmation.
- The legacy seed path runs only for managed git worktrees with pending
seed state. Tests cover the startup condition.
- The rebase preserves the target branch's direct OAuth policy for the
Notion connection flow.
> 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 with the GPT-5 model family assisted this change. The agent
used reasoning, repository tools, code execution, and test execution.
The runtime does not expose the exact model snapshot 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
#` / `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 applications page shows connected services and their status
> - The e2e suite covers the Connections row on that page
> - The server runs a periodic connection health sweep during the test
> - The sweep can change the connected row label and action after the
first render
> - This pull request accepts both connected states on that row
> - The benefit is the test checks the real user path without a sweep
race
## Linked Issues or Issue Description
No public issue exists. This pull request fixes a race in the
applications Connections e2e test.
**Bug:** The test pinned the exact connected-state pill and action.
**Expected:** The test should accept both connected states for the same
connection row.
**Impact:** The health sweep can change the label between assertions.
**Fix:** The test now accepts either label and action on the connected
row.
## What Changed
- Allowed the connected row pill to match `Healthy` or `Needs
attention`.
- Allowed the connected row action to match `Open` or `Reconnect`.
- Kept the not-connected row exact.
## Verification
- `git diff --check
origin/master..origin/test/deflake-applications-crud-health-sweep`
- `git show --stat --summary --oneline
9785785a5d41cd13ee5a0f8aeb73f389cdbdac2e`
- Local Playwright e2e did not run in this worktree.
- CI on this pull request should provide the full proof.
## Risks
- Low risk. The change only widens the expected labels for the connected
row.
- If the UI adds a new state, the test may need another update.
## Model Used
OpenAI GPT-5, tool use, context window not exposed in this shell
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
- [ ] I have updated relevant documentation to reflect my changes
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [ ] I will address all Greptile and reviewer comments before
requesting merge
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip relies on end-to-end tests to catch regressions in the
operator UI
> - The applications list status pill is rendered from more than one
data fetch, so the visible label can lag behind the row itself
> - A default Playwright assertion timeout can expire before the
connections fetch finishes under CI load
> - That creates a flaky failure without changing the underlying product
behavior
> - This pull request extends the two status-pill assertions to use the
longer timeout already used elsewhere in the spec
> - The benefit is the same UI coverage with fewer false negatives
## Linked Issues or Issue Description
There is no public GitHub issue linked to this repo-local fix. This PR
addresses a flaky Playwright assertion in
`tests/e2e/applications-crud.spec.ts`, where the status pill can render
after the default assertion timeout because it depends on the
connections fetch as well as the applications fetch.
## What Changed
- Increased the wait window for the two status-pill visibility
assertions in `tests/e2e/applications-crud.spec.ts`.
- Kept the assertions anchored to the exact expected labels (`Healthy`
and `Not connected`) so the test still verifies the same behavior.
## Verification
- The spec is still discovered cleanly by Playwright.
- The diff stays limited to `tests/e2e/applications-crud.spec.ts`; there
are no product, dependency, or lockfile changes.
- The full browser-backed e2e signal remains CI for this change.
## Risks
- Low risk. This only changes assertion timing in a test file and does
not alter runtime product behavior.
## Model Used
OpenAI Codex, GPT-5, tool-using coding agent.
## 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 control plane people use to manage
AI-agent companies and their governed access to external systems.
> - Connected Apps build on the existing Apps and MCP gateway substrate
so companies can configure reusable, auditable integrations.
> - The current connection record does not yet have a stable public
address, explicit ownership/auth method fields, or subject-specific
credential grants.
> - Without that schema core, later OAuth, per-user authorization, token
brokering, triggers, and connector-service phases cannot enforce tenant
and subject boundaries consistently.
> - This pull request adds the forward-compatible Connections v3 schema
core while preserving the existing connection lifecycle and directly
migrating the remote MCP transport name.
> - The benefit is a company-scoped, least-privilege foundation for
one-click integrations without bypassing Paperclip secrets, profiles,
rules, or audit controls.
## Linked Issues or Issue Description
No matching public issue was found.
**Problem**
Paperclip's current app connections need a durable identity and
authorization substrate before Connected Apps can safely support
multiple setup methods, per-user credentials, provider tenants, and
managed connector services. The existing schema only models a single
connection-level credential set and uses legacy transport terminology.
**Proposed solution**
Add a stable company-scoped connection UID, explicit
ownership/auth/transport fields, a subject-aware `connection_grants`
table, and multi-key credential annotations. Backfill existing
connections and workspace grants in a reversible migration, then update
shared/server/UI contracts to the new `mcp_remote` transport name.
**Related work**
- Related foundation: #9534
- Roadmap: Connected Apps (one-click integrations)
## What Changed
- Added company-scoped connection `uid`, `ownership`, `authKind`, and
canonical transport fields across database, shared contracts,
validators, services, and UI fixtures.
- Added `connection_grants` with workspace/user subject rules, provider
tenant metadata, credential secret refs, revocation state, company
scoping, and uniqueness constraints.
- Added migration `0182_connections_v3_schema_core` to backfill stable
UIDs, rename `remote_http` to `mcp_remote`, infer auth kinds, create
default workspace grants, and support rollback coverage.
- Added multi-key credential annotations and updated gateway/access
services without changing the existing lifecycle behavior.
- Updated the connection glossary, connector playbook, and security
threat model for the new identity, grant, and relay boundaries.
- Added explicit test UIDs to direct database fixtures so the new
non-null invariant is exercised across affected server suites.
## Verification
- `pnpm --filter @paperclipai/shared typecheck`
- `pnpm --filter @paperclipai/db typecheck`
- `pnpm --filter @paperclipai/server typecheck`
- `pnpm --filter @paperclipai/ui typecheck`
- `pnpm exec vitest run server/src/__tests__/tool-access-service.test.ts
server/src/__tests__/tool-gateway-service.test.ts
server/src/__tests__/tool-gateway.test.ts
server/src/__tests__/heartbeat-runtime-skills.test.ts
server/src/__tests__/tool-oauth-legacy-backfill.test.ts
server/src/__tests__/tool-access-policy-service.test.ts
server/src/__tests__/heartbeat-runtime-mcp-servers.test.ts
packages/db/src/connections-v3-schema-core-migration.test.ts
packages/shared/src/validators/tool-access.test.ts --config
vitest.config.ts` — 9 files, 218 tests passed.
- Latest-head GitHub Actions: build, typecheck, general/serialized
suites, backup/worktree restore coverage, both e2e shards, canary,
policy, and security scans pass.
- Greptile: 5/5 with zero unresolved threads.
- `pnpm check:token-gates` remains red only on five pre-existing `#9627`
color literals outside this change.
## Risks
- **Migration risk:** UID backfill and default-grant creation touch
every existing connection. The migration uses company-scoped uniqueness,
deterministic legacy UIDs with ID suffixes, and seeded up/rollback
coverage.
- **Authorization risk:** Grant rows carry credential references.
Constraints enforce workspace-vs-user subject shape, company/connection
lookup indexes, one default grant per connection, and one user grant per
connection/subject. Security review is requested specifically for this
design.
- **Compatibility risk:** `remote_http` is renamed directly to
`mcp_remote`; all repository call sites and fixtures are updated in the
same change.
- **Future-phase risk:** Subject-bound token issuance, triggers, and
connector-service relay verification remain fail-closed requirements
documented for later phases; this PR does not expose those capabilities.
> 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 CLI coding agent. The runtime did not expose an exact
underlying model ID or context-window size; capabilities used include
repository inspection, code editing, shell execution, test execution,
Git/GitHub CLI operations, and structured reasoning.
## 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
> - Governed MCP access spans contracts, runtime enforcement, adapters,
UI surfaces, and operator verification
> - The parity reference PR #9534 is too large for effective automated
or human review
> - The feature therefore needs a linear stack whose individual diffs
stay below the 100-file review limit
> - This pull request is split 8/8 and focuses on end-to-end coverage,
operator docs, evals, and release notes
> - The benefit is a standalone, testable review boundary while
preserving byte-for-byte parity at the top of the stack
## Linked Issues or Issue Description
- Related parity reference: #9534
- Problem: The complete stack needs discoverable browser scenarios,
operator guidance, threat modeling, eval coverage, and a parity proof
before merge.
- Proposed solution: Adds MCP user-story and Smoke Lab e2e suites,
docs/evals/release notes, the skill update, and the root e2e driver
script registration.
- Alternatives considered: keeping #9534 as one 403-file review, or
rewriting the feature to manufacture seams; both were rejected in favor
of path extraction plus compile-driven boundary moves.
- Roadmap alignment: this advances the existing governed MCP/tool-access
work already represented by #9534; it does not introduce a separate
roadmap initiative.
- Stack position: base branch is `pap10341-split/07-ui-apps-activation`.
- Merge policy: merge bottom-up, in order, only after the complete
eight-PR stack has been reviewed and the top-of-stack parity gate
remains empty.
- Requested review: QA for flag audit and e2e/browser acceptance;
Greptile on every PR.
## What Changed
- Adds MCP user-story and Smoke Lab e2e suites, docs/evals/release
notes, the skill update, and the root e2e driver script registration.
- Keeps this PR below 100 changed files and independently typecheckable.
- Preserves the final tree from #9534 when combined with the other seven
stack levels.
## Verification
- `pnpm typecheck`
- `node --check scripts/e2e-mcp-user-stories.mjs`
- `pnpm exec playwright test --config tests/e2e/playwright.config.ts
--list` — 43 tests discovered
- `git diff pap10341-split/08-e2e-docs
6b40e3876d9297105d4ec306e47e46d351c86172` — empty (0 bytes)
## Risks
- Browser suites depend on runtime services and environment setup; this
PR validates discovery locally while QA owns full flag-on/flag-off
execution.
- Stack risk: merging out of order can expose incomplete layers;
mitigate by following the documented bottom-up merge policy.
- Parity risk: later edits to an intermediate branch can drift from
#9534; mitigate by re-running the empty top-of-stack diff 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 Codex, exact model ID `gpt-5.4`; runtime-managed context
window; medium reasoning with repository, shell, Git, GitHub CLI, and
code-execution tools enabled.
## 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] Internal references are omitted except the execution-plan link
explicitly required for this coordinated split stack
- [x] My branch name describes the change 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
## Stack Coordination
- Internal execution plan:
[PAP-13874](/PAP/issues/PAP-13874#document-plan)
- Parity reference: #9534
- Stack: #9556 → #9557 → #9558 → #9559 → #9560 → #9561 → #9562 → #9563
- Merge bottom-up only after full-stack review and an empty parity diff
at #9563.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
Dotta
Nicky Leach