refactor: consolidate project structure and clean up documentation

- Move docs to docs/ (philosophy, roadmap, orchestration scenarios,
  claude integration, testing improvements)
- Strip completed phases from roadmap and claude integration docs
- Move dependencies from requirements*.txt into pyproject.toml
- Move pytest config from pytest.ini into pyproject.toml
- Add Makefile replacing wakeup.sh (setup, run, test, lint, etc.)
- Add CI test gate in Gitea Actions workflow
- Consolidate caches into .cache/ (pytest, mypy, ruff)
- Consolidate build output into build/ (coverage, logs)
- Update Dockerfile for pyproject.toml install
- Update cross-references in README, AGENTS.md, CLAUDE.md

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

docs/testing-improvements.md

@@ -0,0 +1,105 @@
+# Testing Improvements for LLM Outputs
+
+## Problem
+
+LLM outputs are non-deterministic. Tests checking for exact string matches fail when the LLM writes "thirty-seven" instead of "37".
+
+## Proposed Solutions
+
+### 1. LLM-as-Judge Pattern
+
+Use a smaller/faster model to evaluate semantic correctness:
+
+```python
+async def llm_judge(output: str, criteria: str) -> bool:
+    """Use LLM to evaluate if output meets criteria."""
+    prompt = f"""
+    Evaluate if this output is correct:
+    Output: {output}
+    Criteria: {criteria}
+    Answer only YES or NO.
+    """
+    result = await judge_model.run(prompt)
+    return "YES" in result.output.upper()
+
+# Usage in test:
+assert await llm_judge(
+    response,
+    "The answer correctly states that sqrt(144) + 25 = 37"
+)
+```
+
+### 2. Fuzzy/Regex Matching
+
+For numeric answers, accept multiple representations:
+
+```python
+import re
+
+def contains_number(text: str, number: int) -> bool:
+    """Check if text contains number in any form."""
+    patterns = [
+        rf'\b{number}\b',  # Digit form
+        number_to_words(number),  # Word form
+    ]
+    return any(re.search(p, text, re.I) for p in patterns)
+
+# Usage:
+assert contains_number(response, 37)  # Matches "37" or "thirty-seven"
+```
+
+### 3. DeepEval Framework
+
+```python
+from deepeval.metrics import AnswerRelevancyMetric
+from deepeval.test_case import LLMTestCase
+
+def test_calculation():
+    test_case = LLMTestCase(
+        input="What is sqrt(144) + 25?",
+        actual_output=response,
+        expected_output="37"
+    )
+    metric = AnswerRelevancyMetric(threshold=0.7)
+    assert metric.measure(test_case)
+```
+
+### 4. pytest-evals Plugin
+
+Minimal pytest plugin for LLM testing with metrics collection.
+
+```bash
+pip install pytest-evals
+```
+
+### 5. Multiple Runs with Threshold
+
+Run flaky tests multiple times and require majority pass:
+
+```python
+@pytest.mark.flaky(reruns=3, reruns_delay=1)
+def test_llm_response():
+    ...
+```
+
+Or custom:
+
+```python
+@pytest.mark.parametrize("run", range(3))
+def test_llm_response(run):
+    ...
+    # Aggregate results across runs
+```
+
+## Resources
+
+- [DeepEval](https://github.com/confident-ai/deepeval) - LLM evaluation framework
+- [pytest-evals](https://github.com/AlmogBaku/pytest-evals) - pytest plugin for LLM evals
+- [LLM Testing Guide 2025](https://www.confident-ai.com/blog/llm-testing-in-2024-top-methods-and-strategies)
+- [Testing LLM Applications - Langfuse](https://langfuse.com/blog/2025-10-21-testing-llm-applications)
+
+## Implementation Priority
+
+1. Add fuzzy number matching helper (quick win)
+2. Evaluate DeepEval for complex output testing
+3. Consider LLM-as-judge for semantic correctness