Reorganize: Move agentic work to okp_mcp_agent/ subfolder

- Move 59 agentic files to dedicated okp_mcp_agent/ subfolder
- Fix all imports (scripts.* -> relative imports, lightspeed_evaluation.agents -> okp_mcp_agent.core)
- Fix config paths (config/okp_mcp_test_suites -> okp_mcp_agent/config/test_suites)
- Update usage examples in docstrings
- Create TODO.md and IMPORT_FIXES_NEEDED.md documentation
- Create BRANCH_ORGANIZATION_REPORT.md for onboarding

Prepares agent system for migration to okp-mcp repo.
See okp_mcp_agent/TODO.md for migration checklist.

Files moved:
  - agents/ (5 files): okp_mcp_agent.py, llm_advisor, solr_checker, etc.
  - bootstrap/ (5 files): JIRA extraction scripts
  - pattern_discovery/ (3 files): Pattern analysis
  - core/ (4 files): LinuxExpert, SolrExpert, PatternDiscovery
  - tests/ (17 files): All agent tests
  - config/ (35 files): test_suites, patterns, bootstrap artifacts
  - docs/ (10 files): Agent documentation
  - artifacts/ (13 files): Bootstrap run outputs

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

Author: Elle Mackey

.github/workflows/detect-secrets.yaml

@@ -0,0 +1,27 @@
+name: Detect Secrets
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  detect-secrets:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Python version
+        run: python --version
+      - name: Install uv
+        run: pip install --user uv
+      - name: Install dependencies
+        run: uv sync
+      - name: Install devel dependencies
+        run: uv sync --group dev
+      - name: Scan for secrets
+        run: make detect-secrets

.gitignore

@@ -209,3 +209,11 @@ mcp_retrieval_output/
 okp_test_data/
 docs_draft/
 
+# Claude Code cache and project files
+.claude/
+
+# Demo workflow temporary working files (test_pattern_workflow.sh copies these from /tmp/)
+# Note: Versioned pattern files in config/bootstrap_YYYYMMDD/ are kept
+/patterns_report.json
+/config/tickets_with_patterns.yaml
+

AGENTS.md

@@ -49,9 +49,10 @@ Before considering any code change complete, you **MUST** run:
 make black-format
 
 # Run all pre-commit checks at once (same as CI)
-make pre-commit      # Runs: bandit, check-types, pyright, docstyle, ruff, pylint, black-check
+make pre-commit      # Runs: bandit, check-types, pyright, docstyle, ruff, pylint, black-check, detect-secrets
 # or Run each quality checks individually:
 make bandit          # Security scan
+make detect-secrets  # Scan for secrets/credentials
 make check-types     # Type check
 make pyright         # Type check
 make docstyle        # Docstring style

BEST_PRACTICES_TESTING.md

@@ -193,7 +193,7 @@ done
 vim src/okp_mcp/tools.py
 
 # Build and deploy
-podman build -t localhost/okp-mcp:elle .
+podman build -t localhost/okp-mcp:dev .
 # ... deploy to test environment ...
 
 # Run 3 evals