NER-379: Extract store repository facade internals

[freezscholte]

Summary

• Move the remaining forge-store lib.rs behavior into domain modules: repository, internal operation helpers, intents, compare, merge, show, doctor, GC, and cross-domain tests.
• Keep public API paths stable through lib.rs re-exports while reducing lib.rs to a facade under the ADR target.
• Update ADR-0001 and remove the obsolete forge-store lib.rs line-count allowlist entry.

Verification

• scripts/check-rust-line-count.sh
• rtk cargo check -p forge-store
• rtk cargo test -p forge-store
• rtk cargo fmt --all --check
• rtk cargo test --workspace
• rtk cargo clippy --workspace --all-targets -- -D warnings
• rtk bash scripts/ci.sh (PASS=95 FAIL=0)

Linear: NER-379

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