[REFACTOR] applyMigration helper split + non-canonical-file copy

[gradyzhuo]

Summary

Splits the memory-migration logic into smaller, documented helpers and expands what gets carried across when an env's memory dir is migrated between shared and isolated layouts.

• applyMigration now walks every entry under sourceDir:
  • MEMORY.md is special-cased — wrapped as a fragment via the new writeMigrationFragment so the agent picks it up on the next orrery_memory_read and consolidates it without clobbering dest's MEMORY.md.
  • Everything else (user-curated .md files, subdirectories, existing fragments) is copied with skip-existing semantics so dest's existing files are never overwritten.
• writeMigrationFragment records the source content as a migrate-action fragment with id/peer/timestamp/action frontmatter under destDir/fragments/.
• copyTreeSkipExisting recursively copies a tree while preserving destination collisions.
• Source dir is left untouched (non-destructive, reversible if user switches back).

Test plan

• swift test — 143 tests pass (134 baseline + 9 new in MemoryMigrationTests):
  • merge=false is a no-op
  • MEMORY.md from source becomes a fragment in dest
  • Non-canonical .md files copy to dest when missing
  • Existing dest files preserved on collision
  • Subdirectories recursively migrated
  • Existing fragments preserved (skip-existing on fragments dir)

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