[fix] Correct source_file inclusion in rust extractor (#6177)

Previously, source file entries were polluted in the cache that speeds
up directory traversal. Instead of putting only a single directory's
source files in the cache, we were entering the source files for
(potentially) the entire crate.

Fix: only store source files for the current directory, not the whole
crate.

Test: proved that Fuchsia's corpus has no more errors like
"source_file does not have a required_input entry"