Fixes a data-loss bug in the curl install.sh | bash upgrade path. The legacyDeletions pass previously rm -rf'd every listed directory unconditionally, including process-layout content dirs (process/general-plans/reports, process/general-plans/references, and _seeds equivalents). Since install.sh is deterministic (no agent), it cannot run the adaptive safe-migration vc-update Part D performs — so real reports/references content would be destroyed before vc-update ever ran. install.sh now defers any non-empty reports/references dir under process/ (preserved, not deleted) for vc-update to migrate into task folders. Deprecated harness dirs and dead files are still removed. Verified against a real v2.4.1 project: 15 report/reference files preserved, 0 user-content loss.