[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>

ui/src/index.css

@@ -717,15 +717,23 @@ a.paperclip-mention-chip[data-mention-kind="agent"]::before {
   background: none;
 }
 
-/* Copy-to-clipboard button on fenced code blocks */
+/* Actions for fenced and indented preformatted markdown blocks */
 .paperclip-markdown-codeblock {
   position: relative;
 }
 
-.paperclip-markdown-codeblock-copy {
+.paperclip-markdown-codeblock-actions {
   position: absolute;
   top: 0.4rem;
   right: 0.4rem;
+  display: inline-flex;
+  align-items: center;
+  gap: 0.25rem;
+  opacity: 0;
+  transition: opacity 0.12s ease;
+}
+
+.paperclip-markdown-codeblock-action {
   display: inline-flex;
   align-items: center;
   gap: 0.25rem;
@@ -737,30 +745,31 @@ a.paperclip-mention-chip[data-mention-kind="agent"]::before {
   font-size: 0.7rem;
   line-height: 1;
   cursor: pointer;
-  opacity: 0;
-  transition: opacity 0.12s ease, background-color 0.12s ease, color 0.12s ease;
+  transition: background-color 0.12s ease, color 0.12s ease;
 }
 
-.paperclip-markdown-codeblock:hover .paperclip-markdown-codeblock-copy,
-.paperclip-markdown-codeblock-copy:focus-visible,
-.paperclip-markdown-codeblock-copy[data-copied] {
+.paperclip-markdown-codeblock:hover .paperclip-markdown-codeblock-actions,
+.paperclip-markdown-codeblock-actions:focus-within,
+.paperclip-markdown-codeblock-action[data-copied],
+.paperclip-markdown-codeblock-action[data-active] {
   opacity: 1;
 }
 
-.paperclip-markdown-codeblock-copy:hover {
+.paperclip-markdown-codeblock-action:hover {
   background-color: var(--accent);
   color: var(--accent-foreground);
 }
 
-.paperclip-markdown-codeblock-copy[data-copied] {
+.paperclip-markdown-codeblock-action[data-active],
+.paperclip-markdown-codeblock-action[data-copied] {
   color: var(--primary);
 }
 
-.paperclip-markdown-codeblock-copy[data-failed] {
+.paperclip-markdown-codeblock-action[data-failed] {
   color: var(--destructive);
 }
 
-.paperclip-markdown-codeblock-copy-label {
+.paperclip-markdown-codeblock-action-label {
   font-weight: 500;
 }