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.

[Copilot]

Pull request overview

Fixes data loss when reinstalling an extension after specify extension remove --keep-config by preserving top-level extension config files across the install directory wipe-and-recopy behavior in ExtensionManager.install_from_directory.

Changes:

• Capture existing top-level *-config.yml / *-config.local.yml files before removing the destination directory, then restore them after copytree when reinstalling from a directory.
• Add a regression test ensuring a keep-config leftover survives a reinstall that is not a --force overwrite.

Show a summary per file

File	Description
tests/test_extensions.py	Adds regression coverage for reinstall-after-keep-config preservation.
src/specify_cli/extensions/init.py	Preserves *-config*.yml files across reinstall when the extension directory exists but registry reports not installed.

Review details

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• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Low

[Copilot]

Review details

• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Low

[mnriem]

Please address Copilot feedback

[Copilot]

Review details

• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Low

[mnriem]

Please address Copilot feedback and resolve test & lint errors