Add color-coded repository filtering to extract, fix registry resolution bugs, and track file/component provenance

[g5t]

• mccode-antlr extract -l/--list now color-codes output by source and adds REPOSITORY/LOCATION columns; new -r/--repository glob filter selects by originating repository (matches a remote registry's URL or a local registry's root path).
• Fix resolve_registry_and_path's unanchored substring matching, which could misattribute a file to the wrong registry when one registry's filename is a substring of another's (e.g. "Masked_ESS_butterfly.comp" falsely matching a lookup for "ESS_butterfly.comp").
• Deduplicate manifest entries when a file is both embedded and resolvable from a live (e.g. --trust-local-registries) registry.
• Track per-file provenance for embedded dependency files (InMemoryRegistry.origins) and per-component provenance (Comp.origin), so mccode-antlr extract -l can attribute a file/component to its originating local directory even when the original registry isn't currently trusted or resolvable -- without ever exposing a filesystem path.
• Rename tests/reader/in_memory_registry.py to test_in_memory_registry.py: it didn't match pytest's discovery pattern and was silently never run, including in CI.

[g5t]

😨 This was already merged in #303