feat: add Phase 2 schema refinement tools (schema-analyze and schema-refine)

Implemented two new CLI commands for schema analysis and refinement:

1. schema-analyze: Analyzes schemas for rigidity issues
   - Detects exact counts that should be ranges
   - Identifies missing classification system
   - Flags deprecated extensions
   - Calculates rigidity score (0-100)
   - Provides detailed or summary reports

2. schema-refine: Automatically refines rigid schemas
   - Converts exact counts to flexible ranges
   - Rounds overly specific numbers
   - Widens narrow integer constraints
   - Supports dry-run mode
   - Can save to new file or overwrite in place

Key improvements:
- Created SchemaAnalyzer class with issue detection
- Created SchemaRefiner class with automatic fixes
- Improved schema navigation to handle nested properties
- Tested on example schemas (reduced rigidity from 60/100 to 24/100)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

markitect/cli.py

@@ -1872,6 +1872,89 @@ def schema_delete(config, schema_name, confirm):
         sys.exit(1)
 
 
+@cli.command('schema-analyze')
+@click.argument('schema_file', type=click.Path(exists=True))
+@click.option('--verbose', '-v', is_flag=True, help='Show detailed analysis')
+@pass_config
+def schema_analyze_cmd(config, schema_file, verbose):
+    """
+    Analyze a schema for rigidity issues and suggest improvements.
+
+    Examines JSON schemas to detect:
+    - Exact counts that should be ranges
+    - Missing classification system
+    - Deprecated extensions
+    - Overly specific constraints
+
+    Returns exit code 0 for flexible schemas, 1 for rigid schemas, 2 for errors.
+
+    Examples:
+        markitect schema-analyze schema.json
+        markitect schema-analyze schema.json --verbose
+    """
+    from .schema_analyzer import analyze_schema_cli
+    sys.exit(analyze_schema_cli(schema_file, verbose=verbose))
+
+
+@cli.command('schema-refine')
+@click.argument('schema_file', type=click.Path(exists=True))
+@click.option('--output', '-o', type=click.Path(),
+              help='Output file (default: overwrite input file)')
+@click.option('--loosen-counts', is_flag=True, default=True,
+              help='Convert exact counts to flexible ranges (default: enabled)')
+@click.option('--no-loosen-counts', is_flag=True,
+              help='Disable count loosening')
+@click.option('--round-numbers', is_flag=True, default=True,
+              help='Round overly specific numbers (default: enabled)')
+@click.option('--no-round-numbers', is_flag=True,
+              help='Disable number rounding')
+@click.option('--migrate-deprecated', is_flag=True, default=False,
+              help='Migrate deprecated extensions (requires manual review)')
+@click.option('--dry-run', is_flag=True,
+              help='Show changes without applying them')
+@pass_config
+def schema_refine_cmd(config, schema_file, output, loosen_counts, no_loosen_counts,
+                      round_numbers, no_round_numbers, migrate_deprecated, dry_run):
+    """
+    Refine a schema by automatically applying fixes for rigidity issues.
+
+    This command analyzes the schema and applies automatic fixes:
+    - Converts exact counts to flexible ranges
+    - Rounds overly specific numbers
+    - Widens narrow integer constraints
+    - Documents deprecated extension usage
+
+    By default, the input file is overwritten. Use --output to save to a different file.
+
+    Examples:
+        # Refine schema in place
+        markitect schema-refine schema.json
+
+        # Preview changes without applying
+        markitect schema-refine schema.json --dry-run
+
+        # Save refined schema to new file
+        markitect schema-refine schema.json --output refined-schema.json
+
+        # Disable specific refinements
+        markitect schema-refine schema.json --no-loosen-counts
+    """
+    from .schema_refiner import refine_schema_cli
+
+    # Handle flag conflicts
+    loosen = loosen_counts and not no_loosen_counts
+    round_nums = round_numbers and not no_round_numbers
+
+    sys.exit(refine_schema_cli(
+        schema_file,
+        output=output,
+        loosen_counts=loosen,
+        migrate_deprecated=migrate_deprecated,
+        round_numbers=round_nums,
+        dry_run=dry_run
+    ))
+
+
 @cli.command('generate-stub')
 @click.argument('schema_file', type=click.Path(exists=True, path_type=Path))
 @click.option('--output', '-o', type=click.Path(path_type=Path),