A folder of files is not yet a document
Long-form projects benefit from small source files, but readers need a deliberate sequence, consistent outline, resolved links, shared metadata, and one asset namespace. Those concerns belong to a composition model rather than destructive edits across every chapter.
The composition manifest is the source of assembly truth
The portable composition ZIP records inclusion, order, heading offsets, separators, front-matter policy, and profile alongside the source entries. Reordering changes the workbench composition, not imported files on disk; line-level generated-to-source mapping is not included.
Diagnostics should cross the file boundary
Duplicate anchors, reference labels, footnotes, and relative assets appear only when chapters meet. MDLoom reports those collisions at the composition level and attributes each warning to its original source file; line-level mapping is not claimed yet.