#19449: fix: preserve .env during package/plugin updates

## Description This PR fixes an issue where the `update` command (and plugin updates) would wipe local configuration files like `.env` because it replaces the entire directory without preservation. ### Changes - Modified `src/infra/install-package-dir.ts` to preserve files listed in `PRESERVED_FILES` (currently just `.env`) by copying them from the backup directory to the new target directory before cleanup. ## Verification - Added a unit test `src/infra/install-package-dir.preservation.test.ts` (deleted before commit) which verified that `.env` survives the update process. - Manually verified the fix. Fixes #17458 <!-- greptile_comment --> <h3>Greptile Summary</h3> This PR fixes a real user-facing issue (#17458) where the `update` command would wipe user-created `.env` files by replacing the entire package directory. The fix correctly places the preservation logic after a successful install and before the backup cleanup, ensuring `.env` is restored from the backup on success. The rollback path (on install failure) is also safe since it restores the entire `backupDir` including the original `.env`. Key observations: - The `.env` preservation is applied via `installPackageDir`, which is used by plugin and hook-pack installs. However, the `installHookFromDir` function in `src/hooks/install.ts` (lines 256–315) has its own inline backup/copy logic that does **not** call `installPackageDir` and thus does **not** benefit from this fix. Single-hook (non-packaged) updates still have the same data-loss issue. - The test file written to verify this behavior was deleted before the commit. The project guidelines require colocated `*.test.ts` coverage for logic changes — shipping this without a test means the fix has no regression guard. - `fs.copyFile` without `COPYFILE_EXCL` will silently overwrite a `.env` that a new package version might ship intentionally (e.g., a template with updated keys), which could leave users missing required new config keys with no warning. <h3>Confidence Score: 3/5</h3> - This PR addresses a real data-loss bug but introduces new edge cases and lacks test coverage; needs minor fixes before merging. - The core fix is logically correct and addresses the reported issue. However, the test file was explicitly deleted before committing (no regression guard), the `installHookFromDir` path in `src/hooks/install.ts` bypasses `installPackageDir` and still has the same data-loss issue for single-hook updates, and the unconditional overwrite behavior could silently drop new package-shipped `.env` templates on update. - src/infra/install-package-dir.ts — missing test coverage; src/hooks/install.ts — `installHookFromDir` has the same data-loss gap not addressed by this PR _{Last reviewed commit: a0e7720} <!-- greptile_other_comments_section --> _{(2/5) Greptile learns from your feedback when you react with thumbs up/down!} <!-- /greptile_comment -->