fix(ci): diff PR workflow paths from merge base (#4903)

## Thinking Path

> - Paperclip’s PR workflow is part of the control-plane safety surface
because it decides whether a branch is allowed to merge.
> - This issue started in that workflow: the lockfile and manifest
policy checks were diffing `base.sha..head.sha`, which incorrectly
treated unrelated `master` commits as if they belonged to the PR branch.
> - The right fix there is to diff from the PR merge base
(`base...head`) so policy checks only evaluate files introduced by the
branch itself.
> - Once that workflow fix was in place, `/checkpr` exposed a second
blocker on the PR merge ref: `verify` was failing in newer `master`-side
tests that were not part of the original branch diff.
> - The actionable repeated failure came from the ACPX local adapter
test suite, where a test hard-coded the managed Codex home under
`instances/default` even though the stable Vitest runner sets a
non-default `PAPERCLIP_INSTANCE_ID`.
> - This pull request now includes both the original CI diff-scope fix
and the targeted ACPX test fix so the PR’s actual checks align with
current base-branch execution.
> - The benefit is that the original false-positive lockfile failure is
removed, and the merge-ref verify path is hardened against the
instance-id isolation used in CI.

## What Changed

- Updated `.github/workflows/pr.yml` so the lockfile policy and manifest
policy steps diff `pull_request.base.sha...pull_request.head.sha` from
the merge base instead of using a two-dot base/head diff.
- Added an inline workflow comment explaining why the three-dot diff is
required for PR-scoped file detection.
- Updated `packages/adapters/acpx-local/src/server/execute.test.ts` so
the managed Codex home assertion uses a test-specific
`PAPERCLIP_INSTANCE_ID` instead of hard-coding `default`.
- Restored `PAPERCLIP_INSTANCE_ID` after that ACPX test finishes so the
test remains isolated and does not leak process env changes.

## Verification

- Reproduced the original false positive locally by comparing PR heads
`#4901` and `#4902` with the old `base..head` logic; both incorrectly
included `pnpm-lock.yaml` from unrelated `master` commits.
- Verified the new `base...head` logic reduces those PRs to only their
actual changed files and excludes `pnpm-lock.yaml`.
- Verified a real manifest-changing PR (`#4893`) still reports
`package.json` changes under the new logic.
- Ran `pnpm -r typecheck` successfully.
- Ran `pnpm vitest run
packages/adapters/acpx-local/src/server/execute.test.ts` successfully
after the ACPX test fix.
- Ran `pnpm vitest run packages/db/src/backup-lib.test.ts` successfully
against the merge-ref-related DB failure path observed during
`/checkpr`.
- Pushed commit `9520a976` and allowed PR `#4903` checks to rerun on the
updated branch.

## Risks

- Low risk: the workflow change only affects how PR policy checks
determine the changed file set.
- Low risk: the ACPX change is test-only and aligns the test with the
instance-isolation behavior already used by
`scripts/run-vitest-stable.mjs` in CI.
- The remaining operational risk is limited to other unrelated
merge-ref-only failures that were not reproduced in the targeted local
verification above.

> 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-codex`, via the Codex local adapter in Paperclip.
- Tool-using coding model with shell execution, git, GitHub CLI, and
repository inspection in a local worktree.
- Context included the current repo, the Paperclip task thread, PR check
output, and the isolated execution workspace.

## 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
- [ ] 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

.github/workflows/pr.yml

@@ -23,7 +23,9 @@ jobs:
       - name: Block manual lockfile edits
         if: github.head_ref != 'chore/refresh-lockfile'
         run: |
-          changed="$(git diff --name-only "${{ github.event.pull_request.base.sha }}" "${{ github.event.pull_request.head.sha }}")"
+          # Diff the PR branch against its merge base so recent base-branch commits
+          # do not masquerade as changes made by the PR itself.
+          changed="$(git diff --name-only "${{ github.event.pull_request.base.sha }}...${{ github.event.pull_request.head.sha }}")"
           if printf '%s\n' "$changed" | grep -qx 'pnpm-lock.yaml'; then
             echo "Do not commit pnpm-lock.yaml in pull requests. CI owns lockfile updates."
             exit 1
@@ -45,7 +47,7 @@ jobs:
 
       - name: Validate dependency resolution when manifests change
         run: |
-          changed="$(git diff --name-only "${{ github.event.pull_request.base.sha }}" "${{ github.event.pull_request.head.sha }}")"
+          changed="$(git diff --name-only "${{ github.event.pull_request.base.sha }}...${{ github.event.pull_request.head.sha }}")"
           manifest_pattern='(^|/)package\.json$|^pnpm-workspace\.yaml$|^\.npmrc$|^pnpmfile\.(cjs|js|mjs)$'
           if printf '%s\n' "$changed" | grep -Eq "$manifest_pattern"; then
             pnpm install --lockfile-only --ignore-scripts --no-frozen-lockfile

packages/adapters/acpx-local/src/server/execute.test.ts

@@ -176,10 +176,11 @@ describe("acpx_local runtime skill isolation", () => {
     const root = await makeTempRoot();
     const sourceCodexHome = path.join(root, "source-codex-home");
     const paperclipHome = path.join(root, "paperclip-home");
+    const paperclipInstanceId = "test-instance";
     const managedCodexHome = path.join(
       paperclipHome,
       "instances",
-      "default",
+      paperclipInstanceId,
       "companies",
       "company-1",
       "codex-home",
@@ -193,9 +194,11 @@ describe("acpx_local runtime skill isolation", () => {
 
     const previousCodexHome = process.env.CODEX_HOME;
     const previousPaperclipHome = process.env.PAPERCLIP_HOME;
+    const previousPaperclipInstanceId = process.env.PAPERCLIP_INSTANCE_ID;
     try {
       process.env.CODEX_HOME = sourceCodexHome;
       process.env.PAPERCLIP_HOME = paperclipHome;
+      process.env.PAPERCLIP_INSTANCE_ID = paperclipInstanceId;
       await runExecutor({
         agent: "codex",
         stateDir: path.join(root, "state"),
@@ -207,6 +210,8 @@ describe("acpx_local runtime skill isolation", () => {
       else process.env.CODEX_HOME = previousCodexHome;
       if (previousPaperclipHome === undefined) delete process.env.PAPERCLIP_HOME;
       else process.env.PAPERCLIP_HOME = previousPaperclipHome;
+      if (previousPaperclipInstanceId === undefined) delete process.env.PAPERCLIP_INSTANCE_ID;
+      else process.env.PAPERCLIP_INSTANCE_ID = previousPaperclipInstanceId;
     }
 
     const authStat = await fs.lstat(managedAuth);