refactor: simplify WDL module command and resolver internals

[claymcleod]

The module implementation retained unused cache helpers and Git re-exports, while the CLI commands repeated planning and persistence logic. Removed the obsolete resolver code, corrected cache documentation, and shared dependency validation and the add/remove relock-and-write sequence. Lock, update, and upgrade now prepare one plan before branching for dry runs, preserving signer checks, write ordering, and command output.

Added a regression test confirming that remove --no-lock skips resolution of a broken remaining dependency and preserves the existing lockfile byte-for-byte. Local validation passed 357 module library tests, four doctests, and 167 module command tests, plus workspace Clippy with warnings denied, nightly formatting, and spelling checks.

Workspace documentation also built with cargo --locked doc --workspace --no-deps; it reported three existing link warnings in unchanged files. This is an internal refactor; a changelog entry, website update, and lint-rule changes are N/A.

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N/A — internal contribution.

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For PRs containing lint rule changes:

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