feat: Complete Repomix integration with bootstrap --repomix flag

This commit implements issue #8 by adding comprehensive Repomix integration:

- Added RepomixConfigAssessor to assess Repomix configuration and freshness
- Added --repomix flag to bootstrap command to optionally enable Repomix
- Integrated RepomixService into BootstrapGenerator for setup automation
- Created GitHub Actions workflow template for automatic Repomix updates
- Added comprehensive integration and unit tests for Repomix functionality
- Fixed Jinja2 template escaping issues in repomix-update.yml workflow
- Updated Finding constructors in RepomixConfigAssessor to match API
- Fixed unused imports across multiple files (ruff auto-fix)

The --repomix flag allows users to optionally include Repomix configuration
when bootstrapping a repository:

  agentready bootstrap --repomix

This creates:
  - repomix.config.json (Repomix configuration)
  - .repomixignore (ignore patterns)
  - .github/workflows/repomix-update.yml (auto-update workflow)

All tests passing (95/95).

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

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

Author: jeremyeder

src/agentready/assessors/code_quality.py

@@ -1,7 +1,6 @@
 """Code quality assessors for complexity, file length, type annotations, and code smells."""
 
 import subprocess
-from pathlib import Path
 
 from ..models.attribute import Attribute
 from ..models.finding import Citation, Finding, Remediation
@@ -326,7 +325,7 @@ def _assess_python_complexity(self, repository: Repository) -> Finding:
                     self.attribute, reason="No Python code to analyze"
                 )
 
-        except MissingToolError as e:
+        except MissingToolError:
             raise  # Re-raise to be caught by Scanner
         except Exception as e:
             return Finding.error(
@@ -352,7 +351,7 @@ def _assess_with_lizard(self, repository: Repository) -> Finding:
                 self.attribute, reason="Lizard analysis not fully implemented"
             )
 
-        except MissingToolError as e:
+        except MissingToolError:
             raise
         except Exception as e:
             return Finding.error(

src/agentready/assessors/documentation.py

@@ -1,6 +1,5 @@
 """Documentation assessor for CLAUDE.md, README, docstrings, and ADRs."""
 
-from pathlib import Path
 
 from ..models.attribute import Attribute
 from ..models.finding import Citation, Finding, Remediation

src/agentready/assessors/repomix.py

@@ -1,7 +1,8 @@
 """Repomix configuration assessor."""
 
 from ..models.attribute import Attribute
-from ..models.finding import Finding
+from ..models.citation import Citation
+from ..models.finding import Finding, Remediation
 from ..models.repository import Repository
 from ..services.repomix import RepomixService
 from .base import BaseAssessor
@@ -50,14 +51,9 @@ def assess(self, repository: Repository) -> Finding:
 
         # Check if Repomix is configured
         if not service.has_config():
-            return Finding.create_fail(
-                self.attribute,
-                score=0,
-                evidence=[
-                    "Repomix configuration not found",
-                    "Missing repomix.config.json",
-                ],
-                remediation_steps=[
+            remediation = Remediation(
+                summary="Initialize Repomix configuration",
+                steps=[
                     "Initialize Repomix: agentready repomix-generate --init",
                     "Generate context: agentready repomix-generate",
                     "Add to bootstrap: agentready bootstrap --repomix",
@@ -77,62 +73,101 @@ def assess(self, repository: Repository) -> Finding:
                     "agentready repomix-generate --check"
                 ],
                 citations=[
-                    {
-                        "title": "Repomix - AI-Friendly Repository Packager",
-                        "url": "https://github.com/yamadashy/repomix",
-                        "type": "tool",
-                    }
+                    Citation(
+                        source="Repomix GitHub Repository",
+                        title="Repomix - AI-Friendly Repository Packager",
+                        url="https://github.com/yamadashy/repomix",
+                        relevance="Tool for generating AI-optimized repository context",
+                    )
                 ],
             )
+            return Finding(
+                attribute=self.attribute,
+                status="fail",
+                score=0.0,
+                measured_value=None,
+                threshold="Configuration exists",
+                evidence=[
+                    "Repomix configuration not found",
+                    "Missing repomix.config.json",
+                ],
+                remediation=remediation,
+                error_message=None,
+            )
 
         # Check if output exists and is fresh
         output_files = service.get_output_files()
         if not output_files:
-            return Finding.create_fail(
-                self.attribute,
-                score=50,
-                evidence=[
-                    "Repomix configuration exists",
-                    "No Repomix output files found",
-                ],
-                remediation_steps=[
+            remediation = Remediation(
+                summary="Generate Repomix output",
+                steps=[
                     "Generate Repomix output: agentready repomix-generate",
                     "Commit output if needed for team access",
                     "Set up GitHub Action for automatic regeneration",
                 ],
                 tools=["Repomix"],
                 commands=["agentready repomix-generate"],
+                examples=[],
+                citations=[],
+            )
+            return Finding(
+                attribute=self.attribute,
+                status="fail",
+                score=50.0,
+                measured_value=None,
+                threshold="Output files exist and are fresh",
+                evidence=[
+                    "Repomix configuration exists",
+                    "No Repomix output files found",
+                ],
+                remediation=remediation,
+                error_message=None,
             )
 
         # Check freshness (7 days max age)
         is_fresh, message = service.check_freshness(max_age_days=7)
 
         if is_fresh:
             # All good - config exists, output exists and is fresh
-            return Finding.create_pass(
-                self.attribute,
-                score=100,
+            return Finding(
+                attribute=self.attribute,
+                status="pass",
+                score=100.0,
+                measured_value=message,
+                threshold="< 7 days old",
                 evidence=[
                     "Repomix configuration exists",
                     f"{len(output_files)} output file(s) found",
                     message,
                 ],
+                remediation=None,
+                error_message=None,
             )
         else:
             # Config exists, output exists but is stale
-            return Finding.create_fail(
-                self.attribute,
-                score=75,
-                evidence=[
-                    "Repomix configuration exists",
-                    f"{len(output_files)} output file(s) found",
-                    message,
-                ],
-                remediation_steps=[
+            remediation = Remediation(
+                summary="Regenerate Repomix output",
+                steps=[
                     "Regenerate Repomix output: agentready repomix-generate",
                     "Set up GitHub Action for automatic weekly updates",
                     "Add to pre-commit hooks for automatic regeneration",
                 ],
                 tools=["Repomix"],
                 commands=["agentready repomix-generate"],
+                examples=[],
+                citations=[],
+            )
+            return Finding(
+                attribute=self.attribute,
+                status="fail",
+                score=75.0,
+                measured_value=message,
+                threshold="< 7 days old",
+                evidence=[
+                    "Repomix configuration exists",
+                    f"{len(output_files)} output file(s) found",
+                    message,
+                ],
+                remediation=remediation,
+                error_message=None,
             )

src/agentready/assessors/structure.py

@@ -1,6 +1,5 @@
 """Structure assessors for project layout and separation of concerns."""
 
-from pathlib import Path
 
 from ..models.attribute import Attribute
 from ..models.finding import Citation, Finding, Remediation

src/agentready/assessors/stub_assessors.py

@@ -4,10 +4,9 @@
 enhanced later with more sophisticated detection and scoring logic.
 """
 
-from pathlib import Path
 
 from ..models.attribute import Attribute
-from ..models.finding import Citation, Finding, Remediation
+from ..models.finding import Finding, Remediation
 from ..models.repository import Repository
 from .base import BaseAssessor
 

src/agentready/assessors/testing.py

@@ -1,8 +1,5 @@
 """Testing assessors for test coverage, naming conventions, and pre-commit hooks."""
 
-import re
-import subprocess
-from pathlib import Path
 
 from ..models.attribute import Attribute
 from ..models.finding import Citation, Finding, Remediation

src/agentready/cli/bootstrap.py

@@ -21,7 +21,12 @@
     default="auto",
     help="Primary language (default: auto-detect)",
 )
-def bootstrap(repository, dry_run, language):
+@click.option(
+    "--repomix",
+    is_flag=True,
+    help="Initialize Repomix configuration for AI-friendly context generation",
+)
+def bootstrap(repository, dry_run, language, repomix):
     """Bootstrap repository with GitHub infrastructure and best practices.
 
     Creates:
@@ -30,6 +35,7 @@ def bootstrap(repository, dry_run, language):
     - Pre-commit hooks configuration
     - Dependabot configuration
     - Contributing guidelines
+    - Repomix configuration (if --repomix flag is set)
 
     REPOSITORY: Path to git repository (default: current directory)
     """
@@ -44,14 +50,15 @@ def bootstrap(repository, dry_run, language):
     click.echo("=" * 50)
     click.echo(f"\nRepository: {repo_path}")
     click.echo(f"Language: {language}")
+    click.echo(f"Repomix: {repomix}")
     click.echo(f"Dry run: {dry_run}\n")
 
     # Create generator
     generator = BootstrapGenerator(repo_path, language)
 
     # Generate all files
     try:
-        created_files = generator.generate_all(dry_run=dry_run)
+        created_files = generator.generate_all(dry_run=dry_run, enable_repomix=repomix)
     except Exception as e:
         click.echo(f"\nError during bootstrap: {str(e)}", err=True)
         sys.exit(1)

src/agentready/cli/demo.py

@@ -458,10 +458,14 @@ def demo(language, no_browser, keep_repo):
         click.echo()
 
         # Display score with color based on level
-        score_color = "green" if overall_score >= 75 else "yellow" if overall_score >= 60 else "red"
-        click.echo(f"  Overall Score: ", nl=False)
+        score_color = (
+            "green"
+            if overall_score >= 75
+            else "yellow" if overall_score >= 60 else "red"
+        )
+        click.echo("  Overall Score: ", nl=False)
         click.secho(f"{overall_score:.1f}/100", fg=score_color, bold=True)
-        click.echo(f"  Certification: ", nl=False)
+        click.echo("  Certification: ", nl=False)
         click.secho(certification_level, fg=score_color, bold=True)
         click.echo(f"  Assessed:      {assessed}/25 attributes")
         click.echo(f"  Skipped:       {skipped} attributes")
@@ -537,7 +541,7 @@ def demo(language, no_browser, keep_repo):
         click.echo("Next steps:")
         click.echo(f"  • View HTML report: {html_file}")
         click.echo(f"  • View Markdown report: {md_file}")
-        click.echo(f"  • Assess your own repo: agentready assess /path/to/repo")
+        click.echo("  • Assess your own repo: agentready assess /path/to/repo")
         click.echo()
 
         if keep_repo:

src/agentready/cli/main.py

@@ -19,6 +19,7 @@
 
 # Import all assessors
 from ..assessors.documentation import CLAUDEmdAssessor, READMEAssessor
+from ..assessors.repomix import RepomixConfigAssessor
 from ..assessors.structure import StandardLayoutAssessor
 from ..assessors.stub_assessors import (
     ConventionalCommitsAssessor,
@@ -65,6 +66,8 @@ def create_all_assessors():
         ConventionalCommitsAssessor(),
         GitignoreAssessor(),
         CyclomaticComplexityAssessor(),  # Actually Tier 3, but including here
+        # Tier 3 Important (including Repomix)
+        RepomixConfigAssessor(),
     ]
 
     # Add remaining stub assessors

src/agentready/services/bootstrap.py

@@ -6,6 +6,7 @@
 from jinja2 import Environment, PackageLoader, select_autoescape
 
 from .language_detector import LanguageDetector
+from .repomix import RepomixService
 
 
 class BootstrapGenerator:
@@ -42,19 +43,22 @@ def _detect_language(self, language: str) -> str:
         # Return most used language
         return max(languages, key=languages.get).lower()
 
-    def generate_all(self, dry_run: bool = False) -> List[Path]:
+    def generate_all(
+        self, dry_run: bool = False, enable_repomix: bool = False
+    ) -> List[Path]:
         """Generate all bootstrap files.
 
         Args:
             dry_run: If True, don't create files, just return paths
+            enable_repomix: If True, generate Repomix configuration and workflow
 
         Returns:
             List of created file paths
         """
         created_files = []
 
         # GitHub Actions workflows
-        created_files.extend(self._generate_workflows(dry_run))
+        created_files.extend(self._generate_workflows(dry_run, enable_repomix))
 
         # GitHub templates
         created_files.extend(self._generate_github_templates(dry_run))
@@ -68,9 +72,15 @@ def generate_all(self, dry_run: bool = False) -> List[Path]:
         # Contributing guidelines
         created_files.extend(self._generate_docs(dry_run))
 
+        # Repomix configuration (if enabled)
+        if enable_repomix:
+            created_files.extend(self._generate_repomix_config(dry_run))
+
         return created_files
 
-    def _generate_workflows(self, dry_run: bool) -> List[Path]:
+    def _generate_workflows(
+        self, dry_run: bool, enable_repomix: bool = False
+    ) -> List[Path]:
         """Generate GitHub Actions workflows."""
         workflows_dir = self.repo_path / ".github" / "workflows"
         created = []
@@ -101,6 +111,13 @@ def _generate_workflows(self, dry_run: bool) -> List[Path]:
         content = template.render(language=test_language)
         created.append(self._write_file(security_workflow, content, dry_run))
 
+        # Repomix update workflow (if enabled)
+        if enable_repomix:
+            repomix_workflow = workflows_dir / "repomix-update.yml"
+            template = self.env.get_template("workflows/repomix-update.yml.j2")
+            content = template.render()
+            created.append(self._write_file(repomix_workflow, content, dry_run))
+
         return created
 
     def _generate_github_templates(self, dry_run: bool) -> List[Path]:
@@ -177,6 +194,35 @@ def _generate_docs(self, dry_run: bool) -> List[Path]:
 
         return created
 
+    def _generate_repomix_config(self, dry_run: bool) -> List[Path]:
+        """Generate Repomix configuration files.
+
+        Args:
+            dry_run: If True, don't create files, just return paths
+
+        Returns:
+            List of created file paths
+        """
+        created = []
+
+        if not dry_run:
+            # Use RepomixService to generate config and ignore files
+            service = RepomixService(self.repo_path)
+
+            # Generate config (don't overwrite if exists)
+            if service.generate_config(overwrite=False):
+                created.append(service.config_path)
+
+            # Generate ignore file (don't overwrite if exists)
+            if service.generate_ignore(overwrite=False):
+                created.append(service.ignore_path)
+        else:
+            # For dry run, just return the paths that would be created
+            created.append(self.repo_path / "repomix.config.json")
+            created.append(self.repo_path / ".repomixignore")
+
+        return created
+
     def _write_file(self, path: Path, content: str, dry_run: bool) -> Path:
         """Write file to disk or simulate for dry run."""
         if dry_run: