refactor(docs): code analysis engine

changes:
  - file: batch_processor.py
    area: cli
    modified: [BatchProcessor, _process_files]
  - file: output_formatters.py
    area: cli
    modified: [output_batch_toon, output_batch_yaml]

stats:
  lines: "+975/-1527 (net -552)"
  files: 11
  complexity: "Large structural change (normalized)"

Author: tom-sapletta-com

CHANGELOG.md

@@ -124,6 +124,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **Tree-sitter for all** — syntax validation for 165+ languages
 - **Example 07** — comprehensive multi-language demo with 8 languages
 
+## [0.1.13] - 2026-03-23
+
+### Docs
+- Update README.md
+- Update TODO.md
+- Update project/context.md
+
+### Other
+- Update project/analysis.toon
+- Update project/dashboard.html
+- Update project/flow.toon
+- Update project/map.toon
+- Update project/project.toon
+- Update project/project.yaml
+
 ## [0.1.12] - 2026-03-23
 
 ### Docs

README.md

@@ -139,13 +139,13 @@ vallm info
 ### Generate Validation Summary File
 
 ```bash
-# JSON summary for entire project
+# JSON summary for entire project (with per-file details and issues)
 vallm batch . --recursive --format json > validation-summary.json
 
-# YAML summary for src/ directory
+# YAML summary for src/ directory (with per-file details and issues)
 vallm batch src/ --recursive --format yaml > validation-summary.yaml
 
-# TOON format (compact) for CI/CD
+# TOON format (compact, human-readable) with per-file details
 vallm batch . --recursive --format toon > validation-summary.toon
 
 # Text format with security checks
@@ -158,6 +158,96 @@ vallm batch . --recursive --semantic --model qwen2.5-coder:7b --format json > fu
 vallm batch . --recursive --format json | tee validation-summary.json
 ```
 
+**Output Structure (JSON/YAML/TOON formats now include per-file details):**
+
+```json
+{
+  "summary": {
+    "total_files": 146,
+    "passed": 145,
+    "failed": 1
+  },
+  "files": [
+    {
+      "path": "src/proxym/config.py",
+      "language": "python",
+      "verdict": "fail",
+      "score": 0.45,
+      "issues_count": 3,
+      "issues": [
+        {
+          "validator": "syntax",
+          "severity": "error",
+          "message": "Invalid syntax at line 42",
+          "line": 42,
+          "column": 15
+        },
+        {
+          "validator": "imports",
+          "severity": "error", 
+          "message": "Module 'requests' not found",
+          "line": 5,
+          "column": 0
+        }
+      ]
+    }
+  ],
+  "failed_files": [
+    {"path": "src/proxym/config.py", "error": "Validation fail"}
+  ]
+}
+```
+
+```yaml
+---
+summary:
+  total_files: 146
+  passed: 145
+  failed: 1
+
+files:
+  - path: src/proxym/config.py
+    language: python
+    verdict: fail
+    score: 0.45
+    issues_count: 3
+    issues:
+      - validator: syntax
+        severity: error
+        message: "Invalid syntax at line 42"
+        line: 42
+        column: 15
+      - validator: imports
+        severity: error
+        message: "Module 'requests' not found"
+        line: 5
+```
+
+```toon
+# vallm batch | 146f | 145✓ 1✗
+
+SUMMARY:
+  total: 146
+  passed: 145
+  failed: 1
+
+FILES:
+  [python]
+    ✗ src/proxym/config.py
+      verdict: fail
+      score: 0.45
+      issues: 2
+        [error] syntax: Invalid syntax at line 42@42
+        [error] imports: Module 'requests' not found@5
+    ✓ src/proxym/ctl.py
+      verdict: pass
+      score: 0.92
+      issues: 0
+
+FAILED:
+  ✗ src/proxym/config.py: Validation fail
+```
+
 ### Batch Command Options
 
 | Option | Short | Description |

TODO.md

@@ -68,8 +68,8 @@
 
 ## Missing validators (from spec)
 
-- [ ] **LogicalErrorValidator (Tier 1)** — integrate `pyflakes` (already a dependency, not wired up)
-- [ ] **LintValidator (Tier 1)** — integrate `ruff` for style/lint checks via subprocess JSON output
+- [x] **LogicalErrorValidator (Tier 1)** — integrate `pyflakes` (already a dependency, not wired up) ✅ Implemented
+- [x] **LintValidator (Tier 1)** — integrate `ruff` for style/lint checks via subprocess JSON output ✅ Implemented
 - [ ] **RegressionValidator (Tier 4)** — test execution + result comparison via `pytest-json-report`
 - [ ] **TypeCheckValidator (Tier 2)** — `mypy`/`pyright` as optional fast correctness signal
 
@@ -97,6 +97,7 @@
 - [x] **Plugin system tests** - added test coverage for plugin manager in `test_plugins.py`
 - [x] **LogicalErrorValidator** - implemented pyflakes integration in `validators/logical.py`
 - [x] **LintValidator** - implemented ruff integration in `validators/lint.py`
+- [x] **SemanticCache** - implemented caching layer for semantic validation
 - [ ] **Type annotations** — add return types to all public functions; run mypy in CI
 - [ ] **Docstrings** — several internal methods lack docstrings
 - [x] **Tests for semantic validator** - comprehensive test suite exists
@@ -109,4 +110,4 @@
 - [x] **Publish automation** — GitHub Actions workflow for PyPI release on tag
 - [x] **CONTRIBUTING.md** - comprehensive contribution guidelines ✅
 
-Last updated: 2026-03-23
+Last updated: 2026-03-23 (refactoring completed)

VERSION

@@ -1 +1 @@
-0.1.12
+0.1.13