fix: remediate 30 audit findings, bump to v1.2.0

4-agent audit review produced 30 findings (4 Critical, 6 High,
14 Medium, 6 Low). This commit addresses all actionable items:

Critical: version bump 1.1.0→1.2.0, fix type annotation, add Bash
to identify-gem, add AskUserQuestion to 4 agents.

High: tighten mypy config, add Python 3.13 to CI, raise coverage
gate to 50%, update crystal-svg description, fix dangling
origin-premiums cross-reference.

Medium: enhance plugin.json metadata, fix temp file leak in cli.py,
add scope boundaries to overlapping agents, add WebSearch to 2
agents, expand physical-properties and phenomenal-gems skills,
move image instructions to CLAUDE.md, add convenience functions
to __all__, copy CDL spec to docs/.

Low: extend .gitignore, add error handling table and Glob/Grep to
crystal-svg, add confidence scoring to identify-gem, add diamond
scope note to README, create shared test fixtures.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: Bissbert

.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "gemmology",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "Comprehensive coloured gemstone expertise for gemmologists and students, covering identification, properties, grading, treatments, origin determination, and crystal structure visualization with SVG/STL/glTF export. Based on FGA curriculum standards.",
   "author": {
     "name": "Bissbert",
@@ -21,5 +21,9 @@
   ],
   "repository": "https://github.com/gemmology-dev/gemmology-plugin",
   "homepage": "https://gemmology.dev",
-  "lspServers": "./.lsp.json"
+  "lspServers": "./.lsp.json",
+  "license": "MIT",
+  "commands": ["crystal-svg", "identify-gem"],
+  "agents": ["cdl-expert", "crystallography-expert", "documentation-expert", "gemmology-expert", "geometry-expert", "svg-rendering-expert", "test-expert", "twin-law-expert"],
+  "skills": ["chemical-properties", "crystal-visualization", "gem-care-durability", "gem-testing-instruments", "gemstone-species", "grading-valuation", "inclusions-fingerprints", "optical-properties", "origin-determination", "phenomenal-gems", "physical-properties", "synthetics-simulants", "treatments-enhancements"]
 }

.claude/agents/crystallography-expert.md

@@ -9,12 +9,17 @@ tools:
   - WebSearch
   - Glob
   - Grep
+  - AskUserQuestion
 ---
 
 # Crystallography Expert Agent
 
 You are an expert crystallographer assisting with development of the gemmology plugin. Your role is to ensure crystallographic accuracy in all implementations.
 
+## Scope Boundary
+
+Handles crystallographic theory and data accuracy. For computational geometry algorithms → geometry-expert. For twin implementation → twin-law-expert.
+
 ## Expertise
 
 You have deep knowledge of:

.claude/agents/documentation-expert.md

@@ -8,6 +8,8 @@ tools:
   - Bash
   - Glob
   - Grep
+  - AskUserQuestion
+  - WebSearch
 ---
 
 # Documentation Expert Agent

.claude/agents/gemmology-expert.md

@@ -8,6 +8,7 @@ tools:
   - WebSearch
   - Glob
   - Grep
+  - AskUserQuestion
 ---
 
 # Gemmology Expert Agent

.claude/agents/geometry-expert.md

@@ -14,6 +14,10 @@ tools:
 
 You are an expert in 3D computational geometry assisting with development of the gemmology plugin. Your role is to ensure geometric correctness and implement robust algorithms.
 
+## Scope Boundary
+
+Handles computational geometry algorithms. For crystallographic correctness → crystallography-expert. For twinning → twin-law-expert.
+
 ## Expertise
 
 You have deep knowledge of:

.claude/agents/svg-rendering-expert.md

@@ -8,6 +8,7 @@ tools:
   - Edit
   - Glob
   - Grep
+  - WebSearch
 ---
 
 # SVG Rendering Expert Agent

.claude/agents/test-expert.md

@@ -8,6 +8,7 @@ tools:
   - Edit
   - Glob
   - Grep
+  - AskUserQuestion
 ---
 
 # Test Expert Agent

.claude/agents/twin-law-expert.md

@@ -15,6 +15,10 @@ tools:
 
 You are an expert in crystallographic twinning assisting with development of the gemmology plugin. Your role is to ensure twin laws are implemented correctly with accurate geometry.
 
+## Scope Boundary
+
+Handles twin law definition and implementation. For general crystallography → crystallography-expert. For general geometry → geometry-expert.
+
 ## Expertise
 
 You have deep knowledge of:

.github/workflows/ci.yml

@@ -31,7 +31,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
@@ -115,11 +115,11 @@ jobs:
           pip install -e .
 
       - name: Check coverage threshold
-        # Target: 60%, Current threshold: 40% (baseline - cli.py needs tests)
-        run: pytest --cov=src/gemmology_plugin --cov-report=term-missing --cov-fail-under=40
+        # Target: 60%, Current threshold: 50% (baseline - cli.py needs tests)
+        run: pytest --cov=src/gemmology_plugin --cov-report=term-missing --cov-fail-under=50
 
       - name: Coverage report
         run: |
           echo "## Coverage Report" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
-          echo "Current threshold: **40%** (Target: 60%)" >> $GITHUB_STEP_SUMMARY
+          echo "Current threshold: **50%** (Target: 60%)" >> $GITHUB_STEP_SUMMARY

.gitignore

@@ -30,3 +30,18 @@ htmlcov/
 # Build artifacts
 *.db
 *.sqlite
+
+# Ruff
+.ruff_cache/
+
+# Benchmarks
+.benchmarks/
+
+# Heap snapshots
+*.heapsnapshot
+
+# macOS
+.DS_Store
+
+# Environment
+.env