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61a7aeab2a
`install_shared_infra` skipped files that already existed on disk when `force=False`, but the skip branches in both the scripts loop and the templates loop only appended to `skipped_files` without calling `manifest.record_existing`. So when the function ran with a fresh manifest against an already-populated `.specify/` tree (e.g. after the manifest was deleted, corrupted, or extracted out of band), every file went down the skip path, `planned_copies` / `planned_templates` stayed empty, and `manifest.save()` wrote an empty `files` field — leaving the integration believing nothing was installed. Record every skipped file in the manifest, but only when it is not already tracked. This preserves the original hash for files that were previously recorded so `check_modified()` (used by `integration use` to decide whether a user has customized a template) keeps working correctly. Add `TestSpeckitManifestRecordsSkippedFiles` in `tests/integrations/test_integration_claude.py` covering both the fresh-skip path and the recover-after-lost-manifest path. Fixes #2107