feat(mosaic): manifest-owned upgrade guard so updates never wipe operator config (#791) (#802)

packages/mosaic/src/runtime/update-checker.ts

@@ -488,9 +488,13 @@ export function getInstallAllCommand(outdated: PackageUpdateResult[]): string {
 // `mosaic update` installs the new npm CLI but, on its own, leaves the framework
 // files in ~/.config/mosaic/ stale — so shipped launcher/runtime changes (e.g.
 // the agent-name export + native heartbeat) never ACTIVATE until a re-seed.
-// These helpers run the package's own install.sh in sync-only mode (the P4
-// data-safe reconcile: framework-owned overwrite + backup-once; SOUL/USER/
-// *.local/credentials preserved) and, opt-in, relaunch durable agents.
+// These helpers run the package's own install.sh in sync-only mode. The re-seed
+// is manifest-driven (#791): keep mode writes ONLY framework-owned paths from the
+// shared framework-manifest.txt and prunes only retired framework files inside
+// shipped subtrees — every operator path (SOUL/USER/*.local/credentials, fleet
+// roster + agents + backlog, and anything the manifest never anticipated) is
+// left byte-identical. Contract files are still reconciled (overwrite +
+// backup-once). Opt-in, this also relaunches durable agents.
 
 /** Resolve the framework/ directory bundled in the installed package. */
 export function resolveBundledFrameworkRoot(): string {