fix: use relative paths in manifest, .graphify_root, and cache for cross-platform portability (fixes #777)

[adityachaudhary99]

Problem

Three artifacts contained absolute machine-specific paths, breaking git-shared graphify-out/ across different machines and platforms:

1. manifest.json keys
2. .graphify_root content
3. cache/ast/*.json source_file fields

Fix

• save_manifest() — relativizes keys against root via Path.relative_to().as_posix() for POSIX separators
• detect_incremental() — re-anchors relative manifest keys back to absolute using Path() join
• .graphify_root — writes user-provided watch_path (often .) instead of resolved absolute watch_root
• save_cached() / load_cached() — relativize/re-anchor source_file fields in nodes and edges
• _reanchor_source_file() helper in cache.py — handles legacy absolute-path entries
• main.py passes root= to save_manifest() calls

All backward compatible: absolute paths that escape root are preserved as-is in each layer.