fix(coding-agent): keep updating git packages when git clean fails (#11648)

Closes #11597

## Problem

On Windows, `pi update` stopped with `git clean -fdx failed with code 1`
for git extensions such as pi-lens.

1. Another pi session has the extension loaded, so a native module
(`@ast-grep/napi` `.node`) or `ast-grep.exe` is open in that process.
2. npm renames the in-use package dir to
`node_modules/@ast-grep/.napi-win32-x64-msvc-<hash>`. Windows allows the
rename, but npm cannot delete the dir afterwards.
3. The next `pi update` runs `git reset --hard`, then `git clean -fdx`.
git prints `warning: failed to remove ...: Invalid argument` and exits
1.
4. pi threw, leaving the checkout at the new commit with the old
dependencies.

The suggested `-ffdx` does not help. Reproduced locally (git 2.52,
Windows): with a running `.exe`, or a `.node` loaded by another node
process and its dir renamed, both `-fdx` and `-ffdx` fail with `Invalid
argument`. Once the process exits, `-fdx` succeeds.

## Fix

In `cleanAndInstallGitDependencies`, a failed `git clean` no longer
aborts the update. pi:

- prints a warning that files may be in use by another pi session
- still runs `npm install`, so dependencies match the new commit
- keeps the `.pi-update-incomplete` marker, so the next update retries
the clean

## Tests

- `test/git-update.test.ts`: new regression test. A failing clean still
updates and installs dependencies, warns, and keeps the marker. The next
update cleans and removes the marker.
- `test/package-manager.test.ts`: updated the test that expected the
throw.

`npm run check` reports `install-lock is out of date`, and
`package-manager.test.ts > should expand ~ in exclusion and exact
patterns` fails on Windows. Both also happen on `main` without this
change.

packages/coding-agent/CHANGELOG.md

@@ -48,6 +48,7 @@
 - Fixed the external editor failing silently, for example when the editor command is wrong or a Windows editor cannot start from a deep WSL directory. pi now shows a status message such as `External editor exited with code 1; prompt unchanged` ([#11592](https://github.com/earendil-works/pi/issues/11592))
 - Fixed `tool_search` and codemode `searchTools()` ranking a tool below tools that only mention its name in their descriptions, for example `peekaboo app` ranking `mcp__peekaboo__app` 14th. A tool matching more of the query's words now ranks above one matching fewer, a query word in a tool's name scores more than any number of mentions in its description, a tool whose whole name is in the query gets a large bonus, and long server instructions no longer lower the scores of that server's tools ([#11331](https://github.com/earendil-works/pi/issues/11331))
 - Fixed `tool_search` and codemode `searchTools()` finding nothing for Chinese, Japanese, Thai, and other non-ASCII queries, because the tokenizer kept only ASCII letters and digits. Words in any script now match, text without spaces between words such as `搜索记录` is split into words, and canonically equivalent text such as `café` and `cafe\u0301` matches ([#10816](https://github.com/earendil-works/pi/issues/10816), [#11037](https://github.com/earendil-works/pi/pull/11037) by [@haoqixu](https://github.com/haoqixu))
+- Fixed `pi update` stopping with `git clean -fdx failed with code 1` on Windows when another pi session had a git extension's native module or executable open. Windows cannot delete such files, so the update left the new code with the old dependencies. pi now warns, installs the dependencies anyway, and retries the clean on the next update ([#11597](https://github.com/earendil-works/pi/issues/11597))
 
 ### Removed