docs: add SPEC_10 for domain-agnostic refactor

Addresses #75 (Domain Identity Crisis) and #76 (Hardcoded Prompts).

Creates ironclad specification for:
- Centralized DomainConfig in src/config/domain.py
- 15 hardcoded locations to update
- Testing strategy and migration path
- Backwards-compatible rollout

Key insight: Make agent GENERAL by default, with domain presets
for specialization (drug_repurposing, sexual_health, etc.)

docs/specs/SPEC_10_DOMAIN_AGNOSTIC_REFACTOR.md

@@ -0,0 +1,442 @@
+# SPEC_10: Domain-Agnostic Refactor
+
+**Status**: DRAFT
+**Priority**: P1
+**Effort**: Medium (2-3 hours)
+**Related Issues**: #75, #76
+
+## Problem Statement
+
+The codebase has "drug repurposing" hardcoded in **15 locations**:
+
+```
+src/prompts/report.py:11      - SYSTEM_PROMPT
+src/prompts/judge.py:5        - SYSTEM_PROMPT
+src/prompts/judge.py:140      - Evidence scoring prompt
+src/prompts/hypothesis.py:11  - SYSTEM_PROMPT
+src/orchestrators/simple.py:476   - Report header
+src/orchestrators/simple.py:564   - Report header
+src/orchestrators/advanced.py:159 - Task prompt
+src/agents/magentic_agents.py:33  - Agent description
+src/agents/magentic_agents.py:108 - Agent description
+src/agents/search_agent.py:31     - Tool description
+src/agents/tools.py:85            - Tool docstring
+src/mcp_tools.py:27               - Example query
+src/mcp_tools.py:116              - Docstring
+src/mcp_tools.py:164              - Function docstring
+src/mcp_tools.py:167              - Docstring
+```
+
+This violates:
+- **DRY** - Same concept repeated 15 times
+- **Open/Closed** - Can't add domains without modifying multiple files
+- **Flexibility** - Agent is locked to one domain
+
+## Solution: Centralized Domain Configuration
+
+### 1. Create Domain Config Module
+
+**File**: `src/config/domain.py`
+
+```python
+"""Centralized domain configuration for research agents.
+
+This module defines research domains and their associated prompts,
+allowing the agent to operate in domain-agnostic or domain-specific modes.
+
+Usage:
+    from src.config.domain import get_domain_config, ResearchDomain
+
+    # Get default (general) config
+    config = get_domain_config()
+
+    # Get specific domain
+    config = get_domain_config(ResearchDomain.SEXUAL_HEALTH)
+
+    # Use in prompts
+    system_prompt = config.judge_system_prompt
+"""
+
+from enum import Enum
+from typing import ClassVar
+
+from pydantic import BaseModel
+
+
+class ResearchDomain(str, Enum):
+    """Available research domains."""
+
+    GENERAL = "general"
+    DRUG_REPURPOSING = "drug_repurposing"
+    SEXUAL_HEALTH = "sexual_health"
+
+
+class DomainConfig(BaseModel):
+    """Configuration for a research domain.
+
+    Contains all domain-specific text used across the codebase,
+    ensuring consistency and single-source-of-truth.
+    """
+
+    # Identity
+    name: str
+    description: str
+
+    # Report generation
+    report_title: str
+    report_focus: str
+
+    # Judge prompts
+    judge_system_prompt: str
+    judge_scoring_prompt: str
+
+    # Hypothesis prompts
+    hypothesis_system_prompt: str
+
+    # Report writer prompts
+    report_system_prompt: str
+
+    # Search context
+    search_description: str
+    search_example_query: str
+
+    # Agent descriptions (for Magentic mode)
+    search_agent_description: str
+    hypothesis_agent_description: str
+
+
+# ─────────────────────────────────────────────────────────────────
+# Domain Definitions
+# ─────────────────────────────────────────────────────────────────
+
+GENERAL_CONFIG = DomainConfig(
+    name="General Research",
+    description="General-purpose biomedical research agent",
+
+    report_title="## Research Analysis",
+    report_focus="comprehensive research synthesis",
+
+    judge_system_prompt="""You are an expert research judge.
+Your role is to evaluate evidence quality, assess relevance to the research query,
+and determine if sufficient evidence exists to synthesize findings.""",
+
+    judge_scoring_prompt="""Score this evidence for research relevance.
+Provide ONLY scores and extracted data.""",
+
+    hypothesis_system_prompt="""You are a biomedical research scientist.
+Your role is to generate evidence-based hypotheses from the literature,
+identifying key mechanisms, targets, and potential therapeutic implications.""",
+
+    report_system_prompt="""You are a scientific writer specializing in research reports.
+Your role is to synthesize evidence into clear, well-structured reports with
+proper citations and evidence-based conclusions.""",
+
+    search_description="Searches biomedical literature for relevant evidence",
+    search_example_query="metformin aging mechanisms",
+
+    search_agent_description="Searches PubMed, ClinicalTrials.gov, and Europe PMC for evidence",
+    hypothesis_agent_description="Generates mechanistic hypotheses from evidence",
+)
+
+DRUG_REPURPOSING_CONFIG = DomainConfig(
+    name="Drug Repurposing",
+    description="Drug repurposing research specialist",
+
+    report_title="## Drug Repurposing Analysis",
+    report_focus="drug repurposing opportunities",
+
+    judge_system_prompt="""You are an expert drug repurposing research judge.
+Your role is to evaluate evidence for drug repurposing potential, assess
+mechanism plausibility, and determine if compounds warrant further investigation.""",
+
+    judge_scoring_prompt="""Score this evidence for drug repurposing potential.
+Provide ONLY scores and extracted data.""",
+
+    hypothesis_system_prompt="""You are a biomedical research scientist specializing in drug repurposing.
+Your role is to generate mechanistic hypotheses for how existing drugs might
+treat new indications, based on shared pathways and targets.""",
+
+    report_system_prompt="""You are a scientific writer specializing in drug repurposing research reports.
+Your role is to synthesize evidence into actionable drug repurposing recommendations
+with clear mechanistic rationale and clinical translation potential.""",
+
+    search_description="Searches biomedical literature for drug repurposing evidence",
+    search_example_query="metformin alzheimer repurposing",
+
+    search_agent_description="Searches PubMed for drug repurposing evidence",
+    hypothesis_agent_description="Generates mechanistic hypotheses for drug repurposing",
+)
+
+SEXUAL_HEALTH_CONFIG = DomainConfig(
+    name="Sexual Health Research",
+    description="Sexual health and wellness research specialist",
+
+    report_title="## Sexual Health Analysis",
+    report_focus="sexual health and wellness interventions",
+
+    judge_system_prompt="""You are an expert sexual health research judge.
+Your role is to evaluate evidence for sexual health interventions, assess
+efficacy and safety data, and determine clinical applicability.""",
+
+    judge_scoring_prompt="""Score this evidence for sexual health relevance.
+Provide ONLY scores and extracted data.""",
+
+    hypothesis_system_prompt="""You are a biomedical research scientist specializing in sexual health.
+Your role is to generate evidence-based hypotheses for sexual health interventions,
+identifying mechanisms of action and potential therapeutic applications.""",
+
+    report_system_prompt="""You are a scientific writer specializing in sexual health research reports.
+Your role is to synthesize evidence into clear recommendations for sexual health
+interventions with proper safety considerations.""",
+
+    search_description="Searches biomedical literature for sexual health evidence",
+    search_example_query="testosterone therapy female libido",
+
+    search_agent_description="Searches PubMed for sexual health evidence",
+    hypothesis_agent_description="Generates hypotheses for sexual health interventions",
+)
+
+# ─────────────────────────────────────────────────────────────────
+# Domain Registry
+# ─────────────────────────────────────────────────────────────────
+
+DOMAIN_CONFIGS: dict[ResearchDomain, DomainConfig] = {
+    ResearchDomain.GENERAL: GENERAL_CONFIG,
+    ResearchDomain.DRUG_REPURPOSING: DRUG_REPURPOSING_CONFIG,
+    ResearchDomain.SEXUAL_HEALTH: SEXUAL_HEALTH_CONFIG,
+}
+
+# Default domain
+DEFAULT_DOMAIN = ResearchDomain.GENERAL
+
+
+def get_domain_config(domain: ResearchDomain | None = None) -> DomainConfig:
+    """Get configuration for a research domain.
+
+    Args:
+        domain: The research domain. Defaults to GENERAL if None.
+
+    Returns:
+        DomainConfig for the specified domain.
+    """
+    if domain is None:
+        domain = DEFAULT_DOMAIN
+    return DOMAIN_CONFIGS[domain]
+```
+
+### 2. Update Settings to Include Domain
+
+**File**: `src/utils/config.py` (add to Settings class)
+
+```python
+from src.config.domain import ResearchDomain
+
+class Settings(BaseSettings):
+    # ... existing fields ...
+
+    # Domain configuration
+    research_domain: ResearchDomain = ResearchDomain.GENERAL
+```
+
+### 3. Update All 15 Hardcoded Locations
+
+#### 3.1 Prompts Module
+
+**`src/prompts/report.py`**:
+```python
+from src.config.domain import get_domain_config
+
+def get_system_prompt(domain=None):
+    config = get_domain_config(domain)
+    return config.report_system_prompt
+
+# Keep SYSTEM_PROMPT for backwards compatibility
+SYSTEM_PROMPT = get_system_prompt()
+```
+
+**`src/prompts/judge.py`**:
+```python
+from src.config.domain import get_domain_config
+
+def get_system_prompt(domain=None):
+    config = get_domain_config(domain)
+    return config.judge_system_prompt
+
+def get_scoring_prompt(domain=None):
+    config = get_domain_config(domain)
+    return config.judge_scoring_prompt
+
+SYSTEM_PROMPT = get_system_prompt()
+```
+
+**`src/prompts/hypothesis.py`**:
+```python
+from src.config.domain import get_domain_config
+
+def get_system_prompt(domain=None):
+    config = get_domain_config(domain)
+    return config.hypothesis_system_prompt
+
+SYSTEM_PROMPT = get_system_prompt()
+```
+
+#### 3.2 Orchestrators
+
+**`src/orchestrators/simple.py`**:
+```python
+from src.config.domain import get_domain_config
+
+class SimpleOrchestrator:
+    def __init__(self, domain=None, ...):
+        self.domain_config = get_domain_config(domain)
+
+    def _format_report(self, ...):
+        return f"""{self.domain_config.report_title}
+Query: {query}
+...
+"""
+```
+
+**`src/orchestrators/advanced.py`**:
+```python
+from src.config.domain import get_domain_config
+
+async def run_research(..., domain=None):
+    config = get_domain_config(domain)
+    task = f"""Research {config.report_focus} for: {query}
+    ...
+    """
+```
+
+#### 3.3 Agents
+
+**`src/agents/magentic_agents.py`**:
+```python
+from src.config.domain import get_domain_config
+
+def create_search_agent(domain=None):
+    config = get_domain_config(domain)
+    return Agent(
+        description=config.search_agent_description,
+        ...
+    )
+```
+
+**`src/agents/search_agent.py`** and **`src/agents/tools.py`**:
+Similar pattern - inject domain config.
+
+#### 3.4 MCP Tools
+
+**`src/mcp_tools.py`**:
+```python
+from src.config.domain import get_domain_config, ResearchDomain
+
+@mcp.tool
+async def search_pubmed(query: str, domain: str = "general"):
+    """Search PubMed for biomedical literature.
+
+    Args:
+        query: Search query (e.g., "metformin alzheimer")
+        domain: Research domain (general, drug_repurposing, sexual_health)
+    """
+    config = get_domain_config(ResearchDomain(domain))
+    # Use config.search_description in responses
+```
+
+### 4. Update Gradio UI
+
+**`src/app.py`** - Add domain selector:
+
+```python
+from src.config.domain import ResearchDomain, DOMAIN_CONFIGS
+
+domain_dropdown = gr.Dropdown(
+    choices=[d.value for d in ResearchDomain],
+    value="general",
+    label="Research Domain",
+    info="Select research focus area"
+)
+```
+
+## Implementation Checklist
+
+- [ ] Create `src/config/domain.py` with DomainConfig
+- [ ] Add `research_domain` to Settings
+- [ ] Update `src/prompts/report.py`
+- [ ] Update `src/prompts/judge.py`
+- [ ] Update `src/prompts/hypothesis.py`
+- [ ] Update `src/orchestrators/simple.py`
+- [ ] Update `src/orchestrators/advanced.py`
+- [ ] Update `src/agents/magentic_agents.py`
+- [ ] Update `src/agents/search_agent.py`
+- [ ] Update `src/agents/tools.py`
+- [ ] Update `src/mcp_tools.py`
+- [ ] Add domain selector to Gradio UI
+- [ ] Write unit tests for domain config
+- [ ] Update CLAUDE.md, AGENTS.md, GEMINI.md
+
+## Testing Strategy
+
+### Unit Tests
+
+```python
+# tests/unit/config/test_domain.py
+
+def test_get_domain_config_default():
+    config = get_domain_config()
+    assert config.name == "General Research"
+
+def test_get_domain_config_drug_repurposing():
+    config = get_domain_config(ResearchDomain.DRUG_REPURPOSING)
+    assert "drug repurposing" in config.judge_system_prompt.lower()
+
+def test_all_domains_have_required_fields():
+    for domain in ResearchDomain:
+        config = get_domain_config(domain)
+        assert config.report_title
+        assert config.judge_system_prompt
+        assert config.hypothesis_system_prompt
+```
+
+### Integration Tests
+
+```python
+# tests/integration/test_domain_switching.py
+
+@pytest.mark.integration
+async def test_simple_mode_respects_domain():
+    result = await run_simple_mode(
+        "metformin aging",
+        domain=ResearchDomain.GENERAL
+    )
+    assert "## Research Analysis" in result
+
+    result = await run_simple_mode(
+        "metformin aging",
+        domain=ResearchDomain.DRUG_REPURPOSING
+    )
+    assert "## Drug Repurposing Analysis" in result
+```
+
+## Migration Path
+
+1. **Phase 1**: Create domain config, add to Settings (no breaking changes)
+2. **Phase 2**: Update prompts module to use config (backwards compatible)
+3. **Phase 3**: Update orchestrators (backwards compatible via defaults)
+4. **Phase 4**: Update UI with domain selector
+5. **Phase 5**: Update docs and examples
+
+## Success Criteria
+
+- [ ] Zero hardcoded "drug repurposing" strings in `src/`
+- [ ] `grep -r "drug repurposing" src/` returns only `domain.py`
+- [ ] All existing tests pass
+- [ ] New domain can be added by only modifying `domain.py`
+- [ ] Default behavior unchanged (general domain)
+
+## Rollback Plan
+
+All changes are backwards compatible:
+- Default domain = GENERAL (similar to current behavior)
+- Existing APIs unchanged (domain is optional parameter)
+- No database migrations required