feat: add PAM 0.5.0 file-only coverage gate

[Yehonal]

Summary

• add PAM 0.5.0 file-only coverage gate for graph-first retrieval without semantic memory search
• add memory:graph:coverage CLI, coverage scenario, graph aliases/nodes, and runtime documentation
• add the 0.4.0 -> 0.5.0 procedural migration guide

Migration

• Migration guide: migrations/0.4.0-to-0.5.0-file-only-coverage.md
• Graph schema stays pam-graph-v1; this is an optional adoption guide, not a data schema migration.
• Required adoption checks are version metadata, graph validation, coverage scenario, and coverage result classification as PASS / PARTIAL / BLOCKED.

Validation

• npm test: 27/27 passing
• npm run memory:graph:validate: OK
• node tools/memory-graph.mjs coverage --json: 5/5 PASS, hit rate 1.0, 0 partial, 0 blocked
• git diff --check: OK

Performance / read-volume proxy

• File-only PAM-first core read volume: 5 files, 7,914 bytes, token proxy 1,980
• Corpus-first comparison in coverage report: 15 files, 72,268 bytes, token proxy 18,071
• Existing baseline benchmark comparison: markdown 6,655 token proxy -> graph 1,370 token proxy, 79.41% reduction

Privacy

• Coverage and benchmark reports are aggregate-only.
• No raw text, absolute paths, or private paths are included in generated report output.

[Copilot]

Pull request overview

This PR adds PAM 0.5.0 support for a file-only graph coverage gate, helping agents measure graph-first retrieval effectiveness without semantic memory search.

Changes:

• Adds memory:graph:coverage CLI and tests for file-only coverage reporting.
• Adds default coverage scenario, graph nodes/aliases/edges, and runtime/README docs.
• Updates package/version metadata, changelog, and migration guidance for 0.5.0 adoption.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tools/memory-graph.mjs	Implements coverage collection, budgets, CLI flags, and command handling.
tools/test-memory-graph.mjs	Adds tests for coverage output and blocked query classification.
package.json	Bumps package version and adds coverage npm script.
README.md	Documents coverage command and default budget.
benchmarks/file-only-coverage.json	Adds default smoke scenario queries.
memory/pam.version.json	Updates PAM metadata and enables file-only coverage feature flag.
memory/graph/nodes.jsonl	Adds graph nodes for coverage CLI and migration guide.
memory/graph/edges.jsonl	Adds graph relationships for coverage feature.
memory/graph/aliases.jsonl	Adds aliases for coverage-related graph lookup.
memory/graph/catalog.json	Updates graph counts and generation metadata.
memory/agent-memory/pam-runtime.md	Adds file-only efficiency gate guidance.
CHANGELOG.md	Adds 0.5.0 release notes.
migrations/0.4.0-to-0.5.0-file-only-coverage.md	Adds optional adoption guide for the coverage gate.

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