manifest.json records only zero-node files, not the processed corpus

[Nyxx0x]

Version: 0.9.15

After a full extraction of a ~120-file corpus, graphify-out/manifest.json contained exactly 5 entries — precisely the 5 files that produced zero nodes — rather than the set of processed files.

Anything that reads the manifest for change detection or coverage accounting therefore sees a 5-file corpus, and a file that extracted successfully is indistinguishable from a file that was never seen.

Expected

Either the manifest lists every processed file along with its outcome, or the docs state plainly that it is a zero-node/failure report only — in which case the name manifest.json is misleading and something like zero-node-files.json would describe it better.

[safishamsi]

Fixed on v8 in b1e313c (will ship in 0.9.17). The #933 manifest filter compared root-relative node source_files against absolute detect() paths and dropped every fresh semantic doc; both sides are now resolved before comparison, so the manifest records the whole processed corpus and incremental update has a correct baseline. Omitted/zero-node docs stay unstamped so they retry.