fix(shared-infra): refresh_shared_templates preserves recovered user files

[jawwad-ali]

Description

refresh_shared_templates decides whether to skip an existing shared template using only:

if dst.exists() and not force:
    if rel not in tracked_files or rel in modified:
        skipped_files.append(rel); continue

It never consults manifest.is_recovered(rel) — but install_shared_infra does (its _is_managed/is_recovered gate, added by #2918). A recovered file is a pre-existing user file whose on-disk hash was adopted via record_existing(recovered=True), so it is both tracked and hash-unmodified. Both predicates above are therefore false → the file is not skipped → refresh_shared_templates overwrites the user's content with the bundled body.

Reproduced on main @ 92b7cf7: a recovered spec-template.md (# USER CUSTOM CONTENT) is replaced with # BUNDLED CONTENT v2 on a non---force refresh — the exact data-loss class #2918 fixed for install_shared_infra.

Fix

Add the is_recovered check to the skip predicate, mirroring install_shared_infra. One source file, no API change.

Testing

New test_refresh_shared_templates_preserves_recovered_user_file: records a user template as recovered, points the bundled source at a different body, calls refresh_shared_templates(force=False), asserts the user content survives. Fails before (content replaced by bundled body — verified by source-stash), passes after. 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 diffed the refresh skip-predicate against install_shared_infra's is_recovered gate; I reproduced the overwrite, verified fail-before/pass-after, and reviewed the diff.

[Copilot]

Pull request overview

This PR fixes a data-loss edge case in shared template refresh logic by ensuring refresh_shared_templates() treats “recovered” (adopted) files as user-owned and does not overwrite them unless --force is used, aligning behavior with install_shared_infra from #2918.

Changes:

• Update refresh_shared_templates() to skip overwriting templates marked as recovered in the Speckit manifest when force=False.
• Add a regression test that records a user template as recovered and verifies refresh does not clobber its contents.

Show a summary per file

File	Description
src/specify_cli/shared_infra.py	Extend the non-force skip predicate to include manifest.is_recovered(rel) so recovered files are preserved.
tests/integrations/test_cli.py	Add regression test covering recovered-template preservation during refresh.

Review details

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