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Extension archives are unpacked with zipfile.extractall and directory installs are copied; neither restores a stripped Unix mode. A bundled *.sh therefore lands non-executable, so a documented `.specify/extensions/<id>/scripts/bash/foo.sh` invocation fails with "Permission denied" — e.g. a CI step that runs an extension's gate. It only worked incidentally, after a later `specify init`. Restore permissions at the shared sink. Every extension install route funnels through ExtensionManager.install_from_directory (install_from_zip delegates to it; extension add, extension update, and bundle installs all reach it), so calling the existing ensure_executable_scripts() there covers every route — present and future — by construction rather than by patching each command. The helper already makes .specify scripts executable (init, migrate, and integration-install all call it); it is called plainly, re-establishing the same idempotent "scripts are executable" invariant those flows restore. Deliberately the whole-project call rather than a scoped one: a scan-scope argument would only spare re-walking already-correct files — negligible beside the copy/extract just performed — while widening a simple, widely-used interface for a single caller. Existing callers were audited: init's end-of-init call still covers core .specify/scripts and is untouched; integration-install and migrate do no manager install. Nothing is removed. No-op on Windows; best-effort per file; does not change which files are executable or their mode. Tests: a manager-level regression test asserts a mode-0644 script comes out executable via both install_from_directory and install_from_zip(force=True) (the latter also covering the remove-then-reinstall shape of extension update), plus an end-to-end `extension add --dev` test. Both fail without the change; skipped on Windows. Fixes #3722.
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