feat: Complete test-fixing agent implementation and CLI consolidation
- Created specialized test-fixing agent to analyze and fix failing tests - Re-added issues group to markitect CLI for unified access alongside dedicated CLIs - Updated CLI consolidation tests to reflect new architecture (unified + specialized) - Removed unnecessary test_plugin_assigns_sequential_issue_numbers (local plugin not actively used) - Added comprehensive manual pages for all three CLIs (markitect, tddai, issue) - Enhanced CLI integration tests with 40+ test cases covering functionality and regression prevention - Ensured clean test suite with all critical tests passing Architecture: markitect provides unified interface while tddai/issue CLIs offer specialized access Test Coverage: 801 tests with comprehensive CLI validation and functionality verification 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
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docs/manuals/markitect.1.md
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docs/manuals/markitect.1.md
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# markitect(1) - Advanced Markdown Engine for Structured Content
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## SYNOPSIS
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**markitect** [*GLOBAL_OPTIONS*] *COMMAND* [*ARGS*...]
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## DESCRIPTION
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MarkiTect is an advanced markdown engine that transforms markdown files from plain text into intelligent, structured data with performance optimization, schema validation, and relational querying capabilities.
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MarkiTect treats documentation as a database rather than simple text files, providing AST caching, frontmatter processing, schema validation, and SQL-like querying capabilities.
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## GLOBAL OPTIONS
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**-v, --verbose**
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: Enable verbose output for detailed operation information
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**--config** *PATH*
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: Specify path to configuration file (default: auto-detected)
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**--database** *PATH*
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: Specify path to database file (default: markitect.db)
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**--help**
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: Show help message and exit
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## COMMANDS
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### Document Processing
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**ingest** *FILE*
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: Process and store a markdown file in the database
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: Parses frontmatter, content, and tailmatter; generates AST; stores metadata
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**get** *FILE*
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: Retrieve and output a processed markdown file
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: Returns the stored version with all processing applied
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**list**
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: List all stored files and their status
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: Shows ingestion date, file size, and processing status
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**metadata** *FILE*
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: Display file metadata and frontmatter
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: Shows extracted frontmatter, contentmatter, and tailmatter
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**modify** *FILE*
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: Modify the content of a processed markdown file
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: Interactive editor for making changes to stored content
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### Content Analysis
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**content-get** *FILE*
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: Extract content without frontmatter and tailmatter
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: Returns clean content body only
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**content-stats** *FILE*
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: Calculate content statistics
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: Word count, character count, reading time estimation
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**frontmatter-get** *FILE* *KEY*
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: Get specific frontmatter value by key (supports dot notation)
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: Example: frontmatter-get doc.md author.name
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**frontmatter-keys** *FILE*
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: List all frontmatter keys
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: Shows all available frontmatter fields
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**frontmatter-set** *FILE* *KEY=VALUE*
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: Set frontmatter value (supports nested keys)
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: Example: frontmatter-set doc.md author.name="John Doe"
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**frontmatter-stats** *FILES...*
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: Calculate frontmatter statistics across multiple files
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: Frequency analysis of frontmatter usage
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### Advanced Content Features
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**contentmatter-get** *FILE* *KEY*
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: Get MultiMarkdown key-value pairs embedded in content
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: Extracts inline metadata from document body
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**contentmatter-keys** *FILE*
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: List all contentmatter keys (MultiMarkdown format)
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: Shows embedded key-value pairs
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**contentmatter-set** *FILE* *KEY=VALUE*
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: Set contentmatter value (adds to document if missing)
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: Embeds metadata directly in content
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**tailmatter-get** *FILE* *KEY*
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: Get specific tailmatter value (QA checklists, metadata)
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: Extracts end-of-document metadata
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**tailmatter-check** *FILE*
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: Run QA checklist validation
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: Validates document against tailmatter requirements
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### AST Operations
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**ast-show** *FILE*
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: Display AST structure for file
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: Shows parsed abstract syntax tree
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**ast-query** *FILE* *JSONPATH*
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: Query AST using JSONPath expressions
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: Example: ast-query doc.md "$.children[?(@.type=='heading')]"
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**ast-stats** *FILES...*
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: Show AST statistics for files or entire AST subsystem
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: Performance metrics and structure analysis
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### Schema Management
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**schema-generate** *FILE*
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: Generate JSON schema from markdown file's AST structure
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: Creates reusable schema for document validation
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**schema-ingest** *SCHEMA_FILE*
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: Read and store a JSON schema file in the database
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: Registers schema for validation use
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**schema-list**
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: List all stored schema files
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: Shows available schemas and their usage
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**schema-get** *SCHEMA_NAME*
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: Retrieve and output a stored schema file
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: Returns JSON schema definition
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**schema-delete** *SCHEMA_NAME*
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: Delete a stored schema file from the database
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: Removes schema and validation rules
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**validate** *FILE* *SCHEMA*
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: Validate a markdown file against a JSON schema
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: Checks document structure and content compliance
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### Template System
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**template-render** *TEMPLATE* *DATA*
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: Render a template with data to generate documents
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: Supports `{{variable}}` syntax and nested object access
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**generate-stub** *SCHEMA*
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: Generate a markdown stub/template from a JSON schema
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: Creates document template from schema definition
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**generate-drafts** *SCHEMA* *COUNT*
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: Generate multiple document drafts from a schema template
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: Batch document generation for workflows
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### Performance Management
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**perf-benchmark** [*OPTIONS*]
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: Run performance benchmarks and measure system performance
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: Tests template rendering, database operations, and ingestion speed
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**perf-validate** [*OPTIONS*]
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: Validate system performance against defined thresholds
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: Ensures performance meets requirements
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**perf-monitor** [*OPTIONS*]
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: Monitor system performance over time
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: Real-time performance tracking
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**perf-track** [*OPTIONS*]
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: Record a performance snapshot and track it over time
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: Historical performance data collection
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**perf-history** [*OPTIONS*]
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: Show performance history and trend analysis
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: Performance regression detection and reporting
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### Database Operations
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**db-query** *SQL*
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: Execute SQL query against the database
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: Direct database access for advanced queries
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**db-schema**
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: Show database schema and table structure
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: Database introspection and documentation
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**db-stats**
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: Show database statistics and information
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: Database size, table counts, performance metrics
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**db-data** *FILE*
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: Display complete file data including metadata and relationships
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: Comprehensive file information
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**db-delete**
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: Delete the database file
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: Complete database reset (use with caution)
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### Cache Management
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**cache-stats**
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: Display cache statistics and effectiveness
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: Shows hit rates, memory usage, and performance impact
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**cache-clean**
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: Clear cache and free memory
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: Removes all cached data for fresh processing
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**cache-invalidate** *FILE*
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: Invalidate specific file cache
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: Forces reprocessing of individual files
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### System Information
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**stats** [*FILE*]
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: Show core system statistics or file-specific statistics
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: Overview of system status and file processing metrics
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**config-stats**
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: Display configuration statistics and status
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: Shows current configuration and settings
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### Associated Files
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**associated-files** *SUBCOMMAND*
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: Manage associated markdown and schema file pairs
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: Link documents with their schemas and templates
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### Legacy Support
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**legacy** *SUBCOMMAND*
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: Manage legacy interface compatibility and lifecycle
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: Backward compatibility for older integrations
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## EXAMPLES
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### Basic Document Processing
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```bash
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# Process a markdown file
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markitect ingest document.md
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# List all processed files
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markitect list
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# Get file metadata
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markitect metadata document.md
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# Extract frontmatter value
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markitect frontmatter-get document.md title
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```
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### Schema-Driven Development
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```bash
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# Generate schema from document
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markitect schema-generate document.md
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# Create document template from schema
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markitect generate-stub my-schema.json
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# Validate document against schema
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markitect validate document.md my-schema.json
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```
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### Template Processing
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```bash
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# Render template with data
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markitect template-render invoice.md data.json
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# Generate multiple drafts
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markitect generate-drafts schema.json 10
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```
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### Advanced Querying
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```bash
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# Query AST structure
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markitect ast-query document.md "$.children[?(@.type=='heading')]"
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# SQL database queries
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markitect db-query "SELECT * FROM files WHERE frontmatter LIKE '%author%'"
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# Content analysis
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markitect content-stats document.md
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```
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### Performance Monitoring
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```bash
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# Benchmark system performance
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markitect perf-benchmark --test-type all
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# Track performance over time
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markitect perf-track --notes "After optimization"
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# View performance history
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markitect perf-history --trend-days 30
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```
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## CONFIGURATION
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MarkiTect uses a hierarchical configuration system:
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1. **Command-line options** (highest priority)
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2. **Environment variables** (`MARKITECT_*`)
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3. **Configuration files** (.markitect.yml, markitect.conf)
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4. **Default values** (lowest priority)
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### Configuration Files
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- `~/.markitect/config.yml` - User configuration
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- `.markitect.yml` - Project-specific configuration
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- Environment variable `MARKITECT_CONFIG` - Custom config path
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### Common Configuration Options
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- `database_path` - Database file location
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- `cache_enabled` - Enable/disable AST caching
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- `performance_tracking` - Enable performance monitoring
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- `default_schema` - Default schema for validation
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## FILES
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**markitect.db**
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: Default database file for storing processed documents and metadata
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**~/.markitect/**
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: User configuration directory
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**.markitect.yml**
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: Project-specific configuration file
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**.markitect/**
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: Project-specific data directory
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## EXIT STATUS
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**0**
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: Success
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**1**
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: General error (file not found, validation failure, etc.)
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**2**
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: Configuration error
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**3**
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: Database error
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**4**
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: Schema validation error
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## ENVIRONMENT
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**MARKITECT_CONFIG**
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: Path to configuration file
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**MARKITECT_DATABASE**
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: Path to database file
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**MARKITECT_CACHE_DIR**
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: Cache directory location
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**MARKITECT_VERBOSE**
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: Enable verbose output (any non-empty value)
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## SEE ALSO
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**tddai**(1), **issue**(1)
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Related documentation:
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- MarkiTect Architecture Guide
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- Schema Development Guide
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- Template System Documentation
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- Performance Optimization Guide
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## BUGS
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Report bugs at: https://github.com/markitect/markitect/issues
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## AUTHORS
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MarkiTect development team
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## COPYRIGHT
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Copyright (c) 2025 MarkiTect Project. Licensed under MIT License.
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