Replace fixed canonical coverage directories with config-first, analyzer-aware coverage roots

[marco0560]

Replace fixed canonical coverage directories with config-first, analyzer-aware coverage roots

codira currently hard-codes canonical coverage directories as src/, tests/, and scripts/. This is reasonable for many Python repositories, but it is biased toward Python-style layouts and does not
generalize well to Rust, Go, C/C++, JS/TS, mixed-language repositories, or monorepos.

Today there are effectively two different discovery models:

• indexing scope is analyzer-driven via analyzer discovery globs
• coverage scope is hard-coded to src/tests/scripts

This mismatch makes indexing flexible, but keeps coverage policy tied to a Python-centric layout.

Problem

A repository can be fully indexable by active analyzers while still being treated as non-canonical for coverage purposes simply because its sources live outside src/, tests/, or scripts/.

Examples:

• Rust: src/, examples/, benches/
• C/C++: src/, include/, tests/
• Go: packages often live at module root or under custom directories
• monorepos: multiple package roots, not one shared top-level convention

Proposed direction

Adopt a hybrid coverage-root strategy:

1. If codira project config declares coverage roots, use that as the source of truth.
2. Otherwise, fall back to analyzer-defined default coverage roots.
3. For multi-language repos, take the deterministic union of active analyzer defaults.
4. Keep build-file inference advisory only; do not silently make it authoritative.

Why

This keeps behavior deterministic and explicit while removing the current Python-centric hard-code.

It also clarifies semantics:

• indexable = analyzers know how to claim the file
• canonical/coverage-required = the project or analyzer defaults explicitly say this path should be covered

Expected changes

• replace fixed CANONICAL_SOURCE_DIRS coverage policy with config-first resolution
• add analyzer metadata for default coverage roots
• expose resolved coverage roots in CLI JSON output
• preserve deterministic ordering and current strict coverage behavior
• keep uncovered-file auditing, but over resolved coverage roots rather than a fixed tuple

Non-goals

• no fuzzy “guess likely source dirs by name” behavior
• no broad filesystem heuristics replacing explicit policy

Acceptance criteria

• repos can explicitly configure coverage roots
• repos without config use analyzer defaults
• mixed-language repos get deterministic union behavior
• codira cov and codira index --require-full-coverage operate on resolved coverage roots
• existing deterministic reporting remains stable