Indexes primary + reference RO-Crates via ReadROCrateMetadata into a
single id-keyed map and serves the three GraphSource port methods
against it. BFS in build_full_graph follows any reference that
resolves in the merged index, not just ark:-prefixed ones, because
local crates may use bare @ids.

crate_dir_for is a CLI-local affordance (not on the port) so the
SoftwareFetcher can resolve contentUrl paths against the owning crate.

persist_aeg always writes the serialized AnnotatedEvidenceGraph to
output_path. persist_condensed writes the condensed crate only when
--save-condensed was supplied; otherwise it keeps the metadata in
memory for diagnostics (last_condensed_metadata / last_stats) and
returns the condensed id without touching disk.

Source RO-Crate is never modified -- no AppendCrate calls, no
back-pointer injection.

Mirrors the server's asyncCollection task-document shape in process
memory, emits concise progress lines to stdout on step transitions
and per-computation completion, and appends raw LLM responses to a
JSONL trace file when --debug-llm is set.

Tracker calls never raise: observability is a best-effort side
channel, never the reason a pipeline fails.

Resolution order: (1) contentUrl as a file:///<crate-relative-path>
URI resolved against the owning crate directory, (2) GitHub via the
shared prefetch_software_code helper when the URL is an actual HTTP
URL, (3) a "[source not fetched]" placeholder so annotation continues
rather than the run dying on a missing source file.

file:/// URIs are the canonical shape FAIRSCAPE crates use for local
artifacts -- the path after the third slash is crate-relative, not
filesystem-absolute. A bare relative path is also accepted.

prefetch_software_code already returns bracketed placeholders for
non-GitHub or unfetchable URLs; we detect and drop those in favor of
the CLI's own placeholder so the signal stays uniform.

Wires the four local adapters into Condenser + Interpreter and runs
the pipeline against a user-supplied RO-Crate path. --reference is
repeatable and merges additional crates into the graph index for
cross-crate ARK resolution. Default output is
./<rocrate-name>-interpretation.json; --save-condensed and --debug-llm
opt into the condensed-crate sidecar and the JSONL LLM trace.

Adds the interpret_group from fairscape_cli.interpret.command alongside
the other top-level groups (rocrate, import, build, publish, schema,
augment, track). Users can now run `fairscape interpret run <path>`.

pyproject dep + uv.sources path and all import sites under commands/
and interpret/ updated to the renamed package. Behavior unchanged.

See fairscape_graph_tools/EVIDENCE_GRAPH_MIGRATION.md for the coordinated
rename across mds_python, fairscape-cli, and the shared package.