Fixes#777. Relativize manifest keys, .graphify_root, and cache source_file fields on persist; re-anchor on load. In-memory callers still see absolute paths. Symlink round-trip fixed in follow-up commit 8f09326.
style: replace all em dashes with hyphens
fix: explain hidden .graphify/ folder in skill output and README
fix: rename .graphify/ to graphify-out/ so output is visible by default
Dennis Cornwell