model commands amd verification subcommands unnested.

HTML export doesn't mutate model files, it uses tmp folder.
HTML export has artifacts: traces, index, matrix included as header links.

Author: ilijaljubicic

.claude/agents/e2e-test-engineer.md

@@ -144,10 +144,10 @@ When updating tests due to functionality changes:
 3. **Additional detailed queries (when needed):**
    ```bash
    # Get all verifications with full details
-   ./target/debug/reqvire model summary --filter-type="verification" --json > /tmp/all-verifications.json
+   ./target/debug/reqvire summary --filter-type="verification" --json > /tmp/all-verifications.json
 
    # Human-readable list of all verifications
-   ./target/debug/reqvire model summary --filter-type="verification"
+   ./target/debug/reqvire summary --filter-type="verification"
    ```
 
 **Decision Framework:**

.claude/agents/requirements-engineer.md

@@ -222,26 +222,23 @@ specifications/
 # Validate specifications
 reqvire validate [--json]
 
-# Generate model summary with filters
-reqvire model summary [filters] [--json]
+# Generate summary with filters
+reqvire summary [filters] [--json]
 
 # Generate sections summary (files/sections only, no elements)
-reqvire model section-summary [filters] [--json]
-
-# Generate index document
-reqvire model index
+reqvire section-summary [filters] [--json]
 
 # Analyze change impact
 reqvire change-impact --git-commit=<commit> [--json]
 
 # Generate traceability matrix
-reqvire verifications matrix [--json]
+reqvire matrix [--json]
 
 # Generate verification traces
-reqvire verifications traces [--json] [--filter-id=<id>] [--filter-name=<regex>] [--filter-type=<type>]
+reqvire traces [--json] [--filter-id=<id>] [--filter-name=<regex>] [--filter-type=<type>]
 
 # Generate verification coverage report
-reqvire verifications coverage [--json]
+reqvire coverage [--json]
 
 # Format specifications
 reqvire format [--dry-run] [--json]
@@ -269,27 +266,24 @@ reqvire generate-diagrams
 # Full validation with JSON output
 reqvire validate --json > /tmp/validation.json
 
-# Filtered model summary
-reqvire model summary --filter-type="requirement" --filter-is-not-verified --json
+# Filtered summary
+reqvire summary --filter-type="requirement" --filter-is-not-verified --json
 
 # Sections overview (without individual elements)
-reqvire model section-summary --filter-file="specifications/*.md" --json
+reqvire section-summary --filter-file="specifications/*.md" --json
 
 # Change impact analysis
 reqvire change-impact --git-commit=HEAD~1 --json > /tmp/impact.json
-
-# Generate index and save to file
-reqvire model index > index.md
 ```
 
 ## Your Workflow
 
 ### 1. Discovery Phase:
-- Use `reqvire model section-summary --filter-content="security|authentication|authorization"` to understand security requirements in each section
-- Use `reqvire model section-summary --filter-content="performance|latency|throughput"` to identify performance-related requirements
-- Use `reqvire model section-summary --filter-content="validation|verify|test"` to find verification and testing requirements
-- Use `reqvire model section-summary --filter-content="interface|API|integration"` to locate interface requirements
-- Run `reqvire model summary` to understand current state
+- Use `reqvire section-summary --filter-content="security|authentication|authorization"` to understand security requirements in each section
+- Use `reqvire section-summary --filter-content="performance|latency|throughput"` to identify performance-related requirements
+- Use `reqvire section-summary --filter-content="validation|verify|test"` to find verification and testing requirements
+- Use `reqvire section-summary --filter-content="interface|API|integration"` to locate interface requirements
+- Run `reqvire summary` to understand current state
 - Use `reqvire validate --json > /tmp/validation.json` to identify issues
 - Apply filters to focus on specific areas
 
@@ -315,7 +309,7 @@ reqvire model index > index.md
 ## Best Practices
 
 ### Strategic Content Analysis:
-- Use `model section-summary --filter-content` to understand requirement themes in each section before detailed work
+- Use `section-summary --filter-content` to understand requirement themes in each section before detailed work
 - Filter by domain keywords (security, performance, interface) to map requirement distribution
 - Identify sections with specific requirement types to target your analysis effectively
 

.github/workflows/change_impact.yml

@@ -10,7 +10,7 @@ jobs:
       github.event.issue.pull_request != null &&
       (
         contains(github.event.comment.body, '/reqvire impact') ||
-        contains(github.event.comment.body, '/reqvire verifications traces')
+        contains(github.event.comment.body, '/reqvire traces')
       )
     runs-on: ubuntu-latest
 
@@ -89,11 +89,11 @@ jobs:
           echo "$OUTPUT" >> $GITHUB_ENV
           echo "EOF" >> $GITHUB_ENV
 
-      - name: Run Reqvire Verifications Traces (if triggered)
-        if: contains(github.event.comment.body, '/reqvire verifications traces')
+      - name: Run Reqvire Traces (if triggered)
+        if: contains(github.event.comment.body, '/reqvire traces')
         id: run_traces
         run: |
-          OUTPUT=$(./reqvire verifications traces 2>&1 || echo "⚠️ reqvire verifications traces failed.")
+          OUTPUT=$(./reqvire traces 2>&1 || echo "⚠️ reqvire traces failed.")
           echo "REQVIRE_OUTPUT<<EOF" >> $GITHUB_ENV
           echo "$OUTPUT" >> $GITHUB_ENV
           echo "EOF" >> $GITHUB_ENV

.github/workflows/generate_diagrams.yml

@@ -41,11 +41,7 @@ jobs:
       - name: Generate Diagrams
         run: |
           ./reqvire generate-diagrams
-      
-      - name: Generate traces svg
-        run: |
-          ./reqvire verifications traces --svg > specifications/matrix.svg
-                
+
       - name: Check for Changes
         id: check_changes
         run: |

CLAUDE.md

@@ -27,19 +27,18 @@ This guide is split into domain-specific guides for better organization:
 - **Format requirements (preview only)**: `./target/debug/reqvire format --dry-run`
 - **Apply formatting fixes**: `./target/debug/reqvire format`
 - **Generate diagrams**: `./target/debug/reqvire generate-diagrams`
-- **Generate index document**: `./target/debug/reqvire model index > SpecificationIndex.md`
-- **Generate model summary**: `./target/debug/reqvire model summary`
-- **Generate model summary (JSON)**: `./target/debug/reqvire model summary --json > /tmp/model-summary.json`
-- **Generate section summary**: `./target/debug/reqvire model section-summary`
-- **Generate section summary (JSON)**: `./target/debug/reqvire model section-summary --json > /tmp/section-summary.json`
-- **Generate HTML documentation**: `./target/debug/reqvire html --output <OUTPUT_DIR>`
+- **Generate model summary**: `./target/debug/reqvire summary`
+- **Generate model summary (JSON)**: `./target/debug/reqvire summary --json > /tmp/model-summary.json`
+- **Generate section summary**: `./target/debug/reqvire section-summary`
+- **Generate section summary (JSON)**: `./target/debug/reqvire section-summary --json > /tmp/section-summary.json`
+- **Generate HTML documentation**: `./target/debug/reqvire html --output <OUTPUT_DIR>` - Generates HTML output with index, diagrams, traces, coverage, and matrix
 - **Analyze change impact**: `./target/debug/reqvire change-impact --git-commit=<COMMIT_HASH>`
 - **Analyze change impact (JSON)**: `./target/debug/reqvire change-impact --git-commit=HEAD~1 --json > /tmp/impact.json`
-- **Generate verification traces**: `./target/debug/reqvire verifications traces` - Generates upward traceability from verifications to root requirements with Mermaid diagrams
-- **Generate verification traces (JSON)**: `./target/debug/reqvire verifications traces --json > /tmp/verification-traces.json` - JSON output with trace trees for programmatic analysis
-- **Filter verification traces**: `./target/debug/reqvire verifications traces --filter-id=<id>` or `--filter-name=<regex>` or `--filter-type=<type>` - Filter to specific verifications
-- **Generate verification matrix**: `./target/debug/reqvire verifications matrix` - Generates verification traceability matrix
-- **Generate coverage report**: `./target/debug/reqvire verifications coverage` - Generates verification coverage report for leaf requirements
+- **Generate verification traces**: `./target/debug/reqvire traces` - Generates upward traceability from verifications to root requirements with Mermaid diagrams
+- **Generate verification traces (JSON)**: `./target/debug/reqvire traces --json > /tmp/verification-traces.json` - JSON output with trace trees for programmatic analysis
+- **Filter verification traces**: `./target/debug/reqvire traces --filter-id=<id>` or `--filter-name=<regex>` or `--filter-type=<type>` - Filter to specific verifications
+- **Generate verification matrix**: `./target/debug/reqvire matrix` - Generates verification traceability matrix
+- **Generate coverage report**: `./target/debug/reqvire coverage` - Generates verification coverage report for leaf requirements
 
 
 ### Filtering Options