fix(extensions): preserve keep-config leftover on reinstall (data loss)

[jawwad-ali]

Description

extension remove --keep-config deliberately preserves the top-level *-config.yml / *-config.local.yml in the extension dir and drops the registry entry, so the user can reinstall and keep their configuration. But a subsequent install_from_directory silently destroys it:

if dest_dir.exists():
    shutil.rmtree(dest_dir)   # wipes the preserved config
...
if did_remove:                # only runs on the --force path
    ...restore from .backup...

After a keep-config remove the registry reports not installed, so the reinstall is not a --force removal → did_remove is False → the restore block never runs → the config is gone. Reproduced on main @ 92b7cf7: a user config (api_key: MY-CUSTOMIZED-VALUE) survives remove(keep_config=True) but is wiped by the next reinstall — the file doesn't even exist afterward. This is data loss that directly contradicts the feature's promise.

Fix

Before the rmtree, capture any top-level *-config.yml / *-config.local.yml from the existing dest_dir (in-memory), and write them back after the fresh copytree — using the same *-config filter and symlink guard the --force restore path already applies. The --force .backup restore still takes precedence for that path; this only covers the in-place keep-config leftover.

Testing

New test_reinstall_preserves_keep_config_leftover: install → write custom config → remove(keep_config=True) → reinstall (no force) → assert the custom config survives. Fails before (config file gone after reinstall — verified by source-stash), passes after. Full tests/test_extensions.py: 327 passed, 3 skipped (no regressions; keep_config=False/.backup path unaffected). uvx ruff check clean.

AI Disclosure

• I did use AI assistance (describe below)

Found and fixed with Claude Code (Claude Fable 5) under my direction. AI traced the keep-config leftover through the reinstall path and found the restore only fires on --force; I reproduced the data loss, verified fail-before/pass-after and the full suite, and reviewed the diff.