State Modification

DAG Internal State

Dirty Bit: Special vertex '$r3_dirty_bit'

Added when DAG modified
Checked before saving
Cleared after save

Modification Operations:

Adding/updating vertices
Adding/deleting edges
Pruning files
Storing artifacts

Persistence

Saved Data:

All vertices with labels (files + timestamps/metadata)
All edges with labels (dependencies + artifacts)
Version number (currently 4)
Critical metadata

Not Saved:

Dirty bit
Transient state