[bug-fix] Fix reinstall-overwrites-kept-config: preserve config on plain reinstall after --keep-config

[github-actions]

Bug fix — reinstall-overwrites-kept-config

Proposed fix for issue #3427, applying the remediation from the bug assessment.

Verdict: Valid · Severity: medium

Summary

When specify extension remove <ext> --keep-config is used, the extension is unregistered but its *-config.yml files survive in the extension directory. A subsequent plain specify extension add <ext> unconditionally deleted that directory before copying the fresh extension in, silently discarding the preserved config. The fix rescues those stranded config files into memory before the rmtree and writes them back after copytree, so user-customized values always win over the packaged defaults.

Changes

File	Change	Notes
src/specify_cli/extensions/__init__.py	modified	Before rmtree(dest_dir), collect any *-config.yml / *-config.local.yml files from an unregistered dest_dir into memory; restore them after copytree
tests/test_extensions.py	added tests	test_reinstall_after_keep_config_preserves_config and test_reinstall_after_keep_config_preserves_local_config

Tests Added or Updated

• tests/test_extensions.py::TestInstallFromDirectory::test_reinstall_after_keep_config_preserves_config — pins that a customized *-config.yml survives a remove --keep-config → plain reinstall cycle
• tests/test_extensions.py::TestInstallFromDirectory::test_reinstall_after_keep_config_preserves_local_config — same for *-config.local.yml override files

Local Verification

• No project test command could be exercised in this environment (no venv, no pytest available). The logic was verified by code inspection: the fix mirrors the existing backup/restore pattern used by the --force reinstall path, applying it to the previously-unhandled "unregistered but config-bearing directory" case.

Deviations from Assessment

None. The implementation follows the preferred remediation exactly as described.

Risks & Review Notes

• Config files are read into memory; these files are typically < 1 KB so there is no memory concern.
• The not self.registry.is_installed(manifest.id) guard ensures we only rescue configs when the extension is genuinely unregistered, avoiding picking up stale files from a different install.
• The write-back happens after shutil.copytree, so packaged defaults are always superseded by the user's values — no risk of defaults silently winning.
• install_from_zip() delegates to install_from_directory(), so it is covered without additional changes.
• No API surface change; all changes are internal to install_from_directory().

Refs #3427 · cc @grafvonb

• Fixes [Bug]: extension reinstall overwrites config preserved by remove --keep-config #3427

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