* Restore .claude/ and .mcp.json from PR base branch before CLI runs
The CLI's non-interactive mode trusts cwd: it reads .mcp.json and
.claude/settings{,.local}.json from the working directory and acts on
them before any tool-permission gating — executing hooks, setting env
vars (NODE_OPTIONS, LD_PRELOAD), running apiKeyHelper shell commands,
and auto-approving MCP servers. When this action checks out a PR head,
these files are attacker-controlled.
Rather than enumerate dangerous keys, replace the entire .claude/ tree
and .mcp.json with the versions from the PR base branch (which a
maintainer has reviewed). Paths absent on base are deleted. Uses local
git state, so no TOCTOU against the GitHub API.
* Read PR base ref from payload for config restore in agent mode
Agent mode's branchInfo.baseBranch defaults to "main" (or env/input
override) instead of the PR's actual target branch — it doesn't query
prData.baseRefName like tag mode does. This meant a PR targeting
develop would get .claude/ restored from main.
Fix by reading pull_request.base.ref directly from the webhook payload
for pull_request, pull_request_review, and pull_request_review_comment
events. For issue_comment on a PR (no base.ref in payload), fall back
to the mode-provided value — tag mode's value is correct (from GraphQL);
agent mode on issue_comment is an edge case that at worst restores from
the wrong trusted branch, which is still secure.
The payload value passes through validateBranchName for defense-in-depth
(GitHub enforces valid branch names server-side, but we validate anyway).
* Extend restored paths to .gitmodules, .ripgreprc, .claude.json
.gitmodules defines submodule URLs and paths; path-confusion attacks
against git submodule operations can write into .git/hooks. .ripgreprc
can set --pre (arbitrary command on each file) if RIPGREP_CONFIG_PATH
points at it. .claude.json is cheap defense-in-depth.
Documented why .git/ is excluded (not trackable in commits, and
restoring it would undo the PR checkout), along with .gitconfig
(git never reads it from cwd) and shell rc files (sourced from $HOME,
not cwd — checkout cannot reach $HOME).
