Launcher: overlay update instead of rm -rf bin/

The version-sync step wiped ~/.local/share/fluorine/bin/ wholesale
before staging the new bundle in, which destroyed any user content
sitting alongside ours: portable instances (ModOrganizer.ini lives in
bin/ via MO2_BASE_DIR), custom plugins under bin/plugins/, etc.

Replace the wipe with a manifest-driven overlay: orphan top-level
entries we no longer ship get removed, then tar streams the manifested
entries from the extracted bundle on top of the live dir. Existing
directories are kept; user-added files inside our directories survive
because tar -x only writes paths it sees in the input stream.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

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