feat: add API Doc Generator — issue #98

- scripts/api_doc_generator.py: AST-based scanner for scripts/ Python modules
- docs/API.md: generated API reference (33 modules, ~500 lines)
- tests/test_api_doc_generator.py: 12 smoke tests (all passing)

The generator extracts module docstrings and public function signatures (name, args, summary) and produces a markdown table per script. One consolidated document per repo (docs/API.md).

Closes #98

docs/API.md

@@ -0,0 +1,472 @@
+# Compounding Intelligence — Scripts API Reference
+
+*Generated: 2026-04-26 11:02 UTC*
+
+This document auto-documents the public API surface of all scripts
+in `scripts/`. Each section covers one script: module purpose,
+public functions, and their signatures.
+
+---
+
+## `scripts/api_doc_generator.py`
+
+API Doc Generator — Issue #98
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `extract_functions_from_ast` | `extract_functions_from_ast(tree, file_rel)` | Extract public function names, signatures, and first-line doc summaries. |
+| `parse_module` | `parse_module(filepath)` | Parse a Python file and return its module-level docstring and public functions. |
+| `scan_scripts_dir` | `scan_scripts_dir(scripts_dir)` | Scan all .py files in scripts/ and extract API info. |
+| `render_markdown` | `render_markdown(modules)` | Generate full docs/API.md content from the scanned modules. |
+| `render_json` | `render_json(modules)` | Emit machine-readable JSON version of the API reference. |
+| `main` | `main()` | - |
+
+## `scripts/automation_opportunity_finder.py`
+
+Automation Opportunity Finder — Scan fleet for manual processes that could be automated.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `analyze_cron_jobs` | `analyze_cron_jobs(hermes_home)` | Analyze cron job definitions for automation gaps. |
+| `analyze_documents` | `analyze_documents(root_dirs)` | Scan documentation for manual step patterns. |
+| `analyze_scripts` | `analyze_scripts(root_dirs)` | Detect repeated command sequences in scripts. |
+| `analyze_session_transcripts` | `analyze_session_transcripts(session_dirs)` | Find repeated tool-call patterns in session transcripts. |
+| `analyze_shell_history` | `analyze_shell_history(root_dirs)` | Find repeated shell commands from history files. |
+| `deduplicate_proposals` | `deduplicate_proposals(proposals)` | Remove duplicate proposals based on title similarity. |
+| `rank_proposals` | `rank_proposals(proposals)` | Sort proposals by impact * confidence (highest first). |
+| `format_text_report` | `format_text_report(proposals)` | Format proposals as human-readable text. |
+| `main` | `main()` | - |
+
+## `scripts/bootstrapper.py`
+
+Bootstrapper — assemble pre-session context from knowledge store.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `load_index` | `load_index(index_path)` | Load and validate the knowledge index. |
+| `filter_facts` | `filter_facts(facts, repo, agent, include_global)` | Filter facts by repo, agent, and global scope. |
+| `sort_facts` | `sort_facts(facts)` | Sort facts by: confidence (desc), then category priority, then fact text. |
+| `load_repo_knowledge` | `load_repo_knowledge(repo)` | Load per-repo knowledge markdown if it exists. |
+| `load_agent_knowledge` | `load_agent_knowledge(agent)` | Load per-agent knowledge markdown if it exists. |
+| `load_global_knowledge` | `load_global_knowledge()` | Load all global knowledge markdown files. |
+| `render_facts_section` | `render_facts_section(facts, category, label)` | Render a section of facts for a single category. |
+| `estimate_tokens` | `estimate_tokens(text)` | Rough token estimate. |
+| `truncate_to_tokens` | `truncate_to_tokens(text, max_tokens)` | Truncate text to approximately max_tokens, cutting at line boundaries. |
+| `build_bootstrap_context` | `build_bootstrap_context(repo, agent, include_global, max_tokens, index_path)` | Build the full bootstrap context block. |
+| `main` | `main()` | - |
+
+## `scripts/dead_code_detector.py`
+
+Dead Code Detector for Python Codebases
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `is_safe_unused` | `is_safe_unused(name, filepath)` | Check if an unused name is expected to be unused. |
+| `get_git_blame` | `get_git_blame(filepath, lineno)` | Get last author of a line via git blame. |
+| `analyze_file` | `analyze_file(filepath)` | Analyze a single Python file for dead code. |
+| `scan_repo` | `scan_repo(repo_path, exclude_patterns)` | Scan an entire repo for dead code. |
+| `main` | `main()` | - |
+
+## `scripts/dedup.py`
+
+dedup.py — Knowledge deduplication: content hash + semantic similarity.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `normalize_text` | `normalize_text(text)` | Normalize text for hashing: lowercase, collapse whitespace, strip. |
+| `content_hash` | `content_hash(text)` | SHA256 hash of normalized text for exact dedup. |
+| `tokenize` | `tokenize(text)` | Simple tokenizer: lowercase words, 3+ chars. |
+| `token_similarity` | `token_similarity(a, b)` | Token-based Jaccard similarity (0.0-1.0). |
+| `quality_score` | `quality_score(fact)` | Compute quality score for merge ranking. |
+| `merge_facts` | `merge_facts(keep, drop)` | Merge two near-duplicate facts, keeping higher-quality fields. |
+| `dedup_facts` | `dedup_facts(facts, exact_threshold, near_threshold, dry_run)` | Deduplicate a list of knowledge facts. |
+| `dedup_index_file` | `dedup_index_file(input_path, output_path, near_threshold, dry_run)` | Deduplicate an index.json file. |
+| `generate_test_duplicates` | `generate_test_duplicates(n)` | Generate test facts with intentional duplicates for testing. |
+| `main` | `main()` | - |
+
+## `scripts/dependency_graph.py`
+
+Cross-Repo Dependency Graph Builder
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `normalize_repo_name` | `normalize_repo_name(name)` | Normalize a repo name for comparison. |
+| `scan_file_for_deps` | `scan_file_for_deps(filepath, content, own_repo)` | Scan a file's content for references to other repos. |
+| `scan_repo` | `scan_repo(repo_path, repo_name)` | Scan a repo directory for dependencies. |
+| `detect_cycles` | `detect_cycles(graph)` | Detect circular dependencies using DFS. |
+| `to_dot` | `to_dot(graph)` | Generate DOT format output. |
+| `to_mermaid` | `to_mermaid(graph)` | Generate Mermaid format output. |
+| `main` | `main()` | - |
+
+## `scripts/diff_analyzer.py`
+
+Diff Analyzer — Parse unified diffs and categorize every change.
+
+*(no public functions — script runs as `main()` only)*
+
+## `scripts/freshness.py`
+
+Knowledge Freshness Cron — Detect stale entries from code changes (Issue #200)
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `compute_file_hash` | `compute_file_hash(filepath)` | Compute SHA-256 hash of a file. Returns None if file doesn't exist. |
+| `get_git_file_changes` | `get_git_file_changes(repo_path, days)` | Get files changed in git in the last N days. |
+| `load_knowledge_entries` | `load_knowledge_entries(knowledge_dir)` | Load knowledge entries from YAML files in the knowledge directory. |
+| `check_freshness` | `check_freshness(knowledge_dir, repo_root, days)` | Check freshness of knowledge entries against recent code changes. |
+| `update_stale_hashes` | `update_stale_hashes(knowledge_dir, repo_root)` | Update hashes for stale entries. Returns count of updated entries. |
+| `format_report` | `format_report(result, max_items)` | Format freshness check results as a human-readable report. |
+| `main` | `main()` | - |
+
+## `scripts/gitea_issue_parser.py`
+
+Gitea Issue Body Parser — Extract structured data from markdown issue bodies.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `parse_issue_body` | `parse_issue_body(body, title, labels)` | Parse a Gitea issue markdown body into structured JSON. |
+| `fetch_issue_from_url` | `fetch_issue_from_url(url)` | Fetch an issue from a Gitea API URL and parse it. |
+| `main` | `main()` | - |
+
+## `scripts/harvester.py`
+
+harvester.py — Extract durable knowledge from Hermes session transcripts.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `find_api_key` | `find_api_key()` | Find API key from common locations. |
+| `load_extraction_prompt` | `load_extraction_prompt()` | Load the extraction prompt template. |
+| `call_llm` | `call_llm(prompt, transcript, api_base, api_key, model)` | Call the LLM API to extract knowledge from a transcript. |
+| `parse_extraction_response` | `parse_extraction_response(content)` | Parse the LLM response to extract knowledge items. |
+| `load_existing_knowledge` | `load_existing_knowledge(knowledge_dir)` | Load the existing knowledge index. |
+| `fact_fingerprint` | `fact_fingerprint(fact)` | Generate a deduplication fingerprint for a fact. |
+| `deduplicate` | `deduplicate(new_facts, existing, similarity_threshold)` | Remove duplicate facts from new_facts that already exist in the knowledge store. |
+| `validate_fact` | `validate_fact(fact)` | Validate a single knowledge item has required fields. |
+| `write_knowledge` | `write_knowledge(index, new_facts, knowledge_dir, source_session)` | Write new facts to the knowledge store. |
+| `harvest_session` | `harvest_session(session_path, knowledge_dir, api_base, api_key, model, dry_run, min_confidence)` | Harvest knowledge from a single session. |
+| `batch_harvest` | `batch_harvest(sessions_dir, knowledge_dir, api_base, api_key, model, since, limit, dry_run)` | Harvest knowledge from multiple sessions in batch. |
+| `main` | `main()` | - |
+
+## `scripts/improvement_proposals.py`
+
+Improvement Proposal Generator for compounding-intelligence.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `analyze_sessions` | `analyze_sessions(sessions)` | Analyze session data to find waste patterns. |
+| `generate_proposals` | `generate_proposals(patterns, hourly_rate, implementation_overhead)` | Generate improvement proposals from waste patterns. |
+| `format_proposals_markdown` | `format_proposals_markdown(proposals, patterns, generated_at)` | Format proposals as a markdown document. |
+| `format_proposals_json` | `format_proposals_json(proposals)` | Format proposals as JSON. |
+| `main` | `main()` | - |
+
+## `scripts/knowledge_gap_identifier.py`
+
+Knowledge Gap Identifier — Pipeline 10.7
+
+*(no public functions — script runs as `main()` only)*
+
+## `scripts/knowledge_staleness_check.py`
+
+Knowledge Store Staleness Detector — Detect stale knowledge entries by comparing source file hashes.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `compute_file_hash` | `compute_file_hash(filepath)` | Compute SHA-256 hash of a file. Returns None if file doesn't exist. |
+| `check_staleness` | `check_staleness(index_path, repo_root)` | Check all entries in knowledge index for staleness. |
+| `fix_hashes` | `fix_hashes(index_path, repo_root)` | Add hashes to entries missing them. Returns count of fixed entries. |
+| `main` | `main()` | - |
+
+## `scripts/perf_bottleneck_finder.py`
+
+Performance Bottleneck Finder — Identify slow tests, builds, and CI steps.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `find_slow_tests_pytest` | `find_slow_tests_pytest(repo_path)` | Run pytest --durations and parse slow tests. |
+| `find_slow_tests_by_scan` | `find_slow_tests_by_scan(repo_path)` | Scan test files for patterns that indicate slow tests. |
+| `analyze_build_artifacts` | `analyze_build_artifacts(repo_path)` | Find large build artifacts that slow down builds. |
+| `analyze_makefile_targets` | `analyze_makefile_targets(repo_path)` | Analyze Makefile for potentially slow targets. |
+| `analyze_github_actions` | `analyze_github_actions(repo_path)` | Analyze GitHub Actions workflow files for inefficiencies. |
+| `analyze_gitea_ci` | `analyze_gitea_ci(repo_path)` | Analyze Gitea/Drone CI config files. |
+| `find_slow_imports` | `find_slow_imports(repo_path)` | Find Python files with heavy import chains. |
+| `severity_sort_key` | `severity_sort_key(b)` | Sort by severity then duration. |
+| `generate_report` | `generate_report(repo_path)` | Run all analyses and generate a performance report. |
+| `format_markdown` | `format_markdown(report)` | Format report as markdown. |
+| `main` | `main()` | - |
+
+## `scripts/priority_rebalancer.py`
+
+Priority Rebalancer — Re-evaluate issue priorities based on accumulated data.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `collect_knowledge_signals` | `collect_knowledge_signals(knowledge_dir)` | Analyze knowledge store for coverage gaps and staleness. |
+| `collect_staleness_signals` | `collect_staleness_signals(scripts_dir, knowledge_dir)` | Run staleness checker if available. |
+| `collect_metrics_signals` | `collect_metrics_signals(metrics_dir)` | Analyze metrics directory for pipeline health. |
+| `extract_priority` | `extract_priority(labels)` | Extract priority level from issue labels. |
+| `compute_issue_score` | `compute_issue_score(issue, repo, signals, now)` | Compute priority score for a single issue. |
+| `generate_report` | `generate_report(scores, signals, org, repos_scanned)` | Generate the full priority report. |
+| `generate_markdown_report` | `generate_markdown_report(report)` | Generate human-readable markdown report. |
+| `main` | `main()` | - |
+
+## `scripts/refactoring_opportunity_finder.py`
+
+Finds refactoring opportunities in codebases
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `compute_file_complexity` | `compute_file_complexity(filepath)` | Compute cyclomatic complexity for a Python file. |
+| `calculate_refactoring_score` | `calculate_refactoring_score(metrics)` | Calculate a refactoring priority score (0-100) based on file metrics. |
+| `scan_directory` | `scan_directory(directory, extensions)` | Scan directory for source files. |
+| `generate_proposals` | `generate_proposals(directory, min_score)` | Generate refactoring proposals by analyzing source files. |
+| `main` | `main()` | - |
+
+## `scripts/sampler.py`
+
+sampler.py — Score and rank sessions by harvest value.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `scan_session_fast` | `scan_session_fast(path)` | Extract scoring metadata from a session without parsing the full JSONL. |
+| `parse_session_timestamp` | `parse_session_timestamp(filename)` | Parse timestamp from session filename. |
+| `score_session` | `score_session(meta, now, seen_repos)` | Score a session for harvest value. Returns (score, breakdown). |
+| `main` | `main()` | - |
+
+## `scripts/session_metadata.py`
+
+session_metadata.py - Extract structured metadata from Hermes session transcripts.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `extract_session_metadata` | `extract_session_metadata(file_path)` | Extract structured metadata from a Hermes session JSONL transcript. |
+| `process_session_directory` | `process_session_directory(directory_path, output_file)` | Process all JSONL files in a directory. |
+| `main` | `main()` | CLI entry point. |
+
+## `scripts/session_pair_harvester.py`
+
+Session Transcript → Training Pair Harvester
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `compute_hash` | `compute_hash(text)` | Content hash for deduplication. |
+| `extract_pairs_from_session` | `extract_pairs_from_session(session_data, min_ratio, min_response_words)` | Extract terse→rich pairs from a single session object. |
+| `extract_from_jsonl_file` | `extract_from_jsonl_file(filepath, **kwargs)` | Extract pairs from a session JSONL file. |
+| `deduplicate_pairs` | `deduplicate_pairs(pairs)` | Remove duplicate pairs across files. |
+| `main` | `main()` | - |
+
+## `scripts/session_reader.py`
+
+session_reader.py — Parse Hermes session JSONL transcripts.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `read_session` | `read_session(path)` | Read a session JSONL file and return all messages as a list. |
+| `read_session_iter` | `read_session_iter(path)` | Iterate over session messages without loading all into memory. |
+| `extract_conversation` | `extract_conversation(messages)` | Extract user/assistant conversation turns, skipping tool-only messages. |
+| `truncate_for_context` | `truncate_for_context(messages, head, tail)` | Truncate long sessions: keep first N + last N messages. |
+| `messages_to_text` | `messages_to_text(messages)` | Convert message list to plain text for LLM consumption. |
+| `get_session_metadata` | `get_session_metadata(path)` | Extract metadata from a session file (first message often has config info). |
+
+## `scripts/test_automation_opportunity_finder.py`
+
+Tests for scripts/automation_opportunity_finder.py — 8 tests.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_analyze_cron_jobs_no_file` | `test_analyze_cron_jobs_no_file()` | Returns empty list when no cron jobs file exists. |
+| `test_analyze_cron_jobs_disabled` | `test_analyze_cron_jobs_disabled()` | Detects disabled cron jobs. |
+| `test_analyze_cron_jobs_errors` | `test_analyze_cron_jobs_errors()` | Detects cron jobs with error status. |
+| `test_analyze_documents_finds_todos` | `test_analyze_documents_finds_todos()` | Detects TODO markers in documents. |
+| `test_analyze_scripts_repeated_commands` | `test_analyze_scripts_repeated_commands()` | Detects repeated shell commands across scripts. |
+| `test_analyze_session_transcripts` | `test_analyze_session_transcripts()` | Detects repeated tool-call sequences. |
+| `test_deduplicate_proposals` | `test_deduplicate_proposals()` | Deduplicates proposals with similar titles. |
+| `test_rank_proposals` | `test_rank_proposals()` | Ranks proposals by impact * confidence. |
+
+## `scripts/test_bootstrapper.py`
+
+Tests for bootstrapper.py — context assembly from knowledge store.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `make_index` | `make_index(facts, tmp_dir)` | Create a temporary index.json with given facts. |
+| `test_empty_index` | `test_empty_index()` | Empty knowledge store produces graceful output. |
+| `test_filter_by_repo` | `test_filter_by_repo()` | Filter facts by repository. |
+| `test_filter_by_agent` | `test_filter_by_agent()` | Filter facts by agent type. |
+| `test_no_global_flag` | `test_no_global_flag()` | Excluding global facts works. |
+| `test_sort_by_confidence` | `test_sort_by_confidence()` | Facts sort by confidence descending. |
+| `test_sort_pitfalls_first` | `test_sort_pitfalls_first()` | Pitfalls sort before facts at same confidence. |
+| `test_truncate_to_tokens` | `test_truncate_to_tokens()` | Truncation cuts at line boundary. |
+| `test_estimate_tokens` | `test_estimate_tokens()` | Token estimation is reasonable. |
+| `test_build_full_context` | `test_build_full_context()` | Full context with facts renders correctly. |
+| `test_max_tokens_respected` | `test_max_tokens_respected()` | Output respects max_tokens limit. |
+| `test_missing_index_graceful` | `test_missing_index_graceful()` | Missing index.json doesn't crash. |
+
+## `scripts/test_diff_analyzer.py`
+
+Tests for scripts/diff_analyzer.py — 10 tests.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_empty` | `test_empty()` | - |
+| `test_addition` | `test_addition()` | - |
+| `test_deletion` | `test_deletion()` | - |
+| `test_modification` | `test_modification()` | - |
+| `test_rename` | `test_rename()` | - |
+| `test_multiple_files` | `test_multiple_files()` | - |
+| `test_binary` | `test_binary()` | - |
+| `test_to_dict` | `test_to_dict()` | - |
+| `test_context_only` | `test_context_only()` | - |
+| `test_multi_hunk` | `test_multi_hunk()` | - |
+| `run_all` | `run_all()` | - |
+
+## `scripts/test_gitea_issue_parser.py`
+
+Tests for scripts/gitea_issue_parser.py
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_basic_parsing` | `test_basic_parsing()` | - |
+| `test_numbered_criteria` | `test_numbered_criteria()` | - |
+| `test_epic_ref_from_body` | `test_epic_ref_from_body()` | - |
+| `test_empty_body` | `test_empty_body()` | - |
+| `test_no_sections` | `test_no_sections()` | - |
+| `test_multiple_sections` | `test_multiple_sections()` | - |
+| `run_all` | `run_all()` | - |
+
+## `scripts/test_harvest_prompt.py`
+
+Test harness for knowledge extraction prompt.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `validate_knowledge_item` | `validate_knowledge_item(item, idx)` | Validate a single knowledge item. Returns list of errors. |
+| `validate_extraction` | `validate_extraction(data)` | Validate a full extraction result. Returns (is_valid, errors, warnings). |
+| `validate_transcript_coverage` | `validate_transcript_coverage(data, transcript)` | Check that extracted facts are actually supported by the transcript. |
+| `run_tests` | `run_tests()` | Run the built-in test suite. |
+| `validate_file` | `validate_file(filepath)` | Validate an existing extraction JSON file. |
+
+## `scripts/test_harvest_prompt_comprehensive.py`
+
+Comprehensive tests for knowledge extraction prompt.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `check_prompt_structure` | `check_prompt_structure()` | - |
+| `check_confidence_scoring` | `check_confidence_scoring()` | - |
+| `check_example_quality` | `check_example_quality()` | - |
+| `check_constraint_coverage` | `check_constraint_coverage()` | - |
+| `check_test_sessions` | `check_test_sessions()` | - |
+| `test_prompt_structure` | `test_prompt_structure()` | - |
+| `test_confidence_scoring` | `test_confidence_scoring()` | - |
+| `test_example_quality` | `test_example_quality()` | - |
+| `test_constraint_coverage` | `test_constraint_coverage()` | - |
+| `test_test_sessions` | `test_test_sessions()` | - |
+
+## `scripts/test_harvester_pipeline.py`
+
+Smoke test for harvester pipeline — verifies the full chain:
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_session_reader` | `test_session_reader()` | Test that session_reader parses JSONL correctly. |
+| `test_validate_fact` | `test_validate_fact()` | Test fact validation. |
+| `test_deduplicate` | `test_deduplicate()` | Test deduplication. |
+| `test_knowledge_store_roundtrip` | `test_knowledge_store_roundtrip()` | Test loading and writing knowledge index. |
+| `test_full_chain_no_llm` | `test_full_chain_no_llm()` | Test the full pipeline minus the LLM call. |
+
+## `scripts/test_improvement_proposals.py`
+
+Tests for scripts/improvement_proposals.py — 15 tests.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_empty_sessions` | `test_empty_sessions()` | - |
+| `test_no_patterns_on_clean_sessions` | `test_no_patterns_on_clean_sessions()` | - |
+| `test_repeated_error_detection` | `test_repeated_error_detection()` | Same error across 3+ sessions triggers pattern. |
+| `test_repeated_error_threshold` | `test_repeated_error_threshold()` | 2 occurrences should NOT trigger (threshold is 3). |
+| `test_slow_tool_detection` | `test_slow_tool_detection()` | Tool with avg latency > 5000ms across 5+ calls. |
+| `test_fast_tool_not_flagged` | `test_fast_tool_not_flagged()` | Tool under 5000ms avg should not trigger. |
+| `test_failed_retry_detection` | `test_failed_retry_detection()` | 3+ consecutive calls to same tool triggers retry pattern. |
+| `test_manual_process_detection` | `test_manual_process_detection()` | 10+ tool calls with <= 3 unique tools. |
+| `test_generate_proposals_from_patterns` | `test_generate_proposals_from_patterns()` | Proposals generated from waste patterns. |
+| `test_proposal_roi_positive` | `test_proposal_roi_positive()` | ROI weeks should be a positive number for recoverable time. |
+| `test_proposals_sorted_by_impact` | `test_proposals_sorted_by_impact()` | Proposals should be sorted by monthly hours saved (descending). |
+| `test_format_markdown` | `test_format_markdown()` | Markdown output should contain expected sections. |
+| `test_format_json` | `test_format_json()` | JSON output should be valid and parseable. |
+| `test_normalize_error` | `test_normalize_error()` | Error normalization should remove paths and hashes. |
+| `test_cli_integration` | `test_cli_integration()` | End-to-end test: write input JSON, run script, check output. |
+| `run_all` | `run_all()` | - |
+
+## `scripts/test_knowledge_staleness.py`
+
+Tests for scripts/knowledge_staleness_check.py — 8 tests.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_fresh_entry` | `test_fresh_entry()` | - |
+| `test_stale_entry` | `test_stale_entry()` | - |
+| `test_missing_source` | `test_missing_source()` | - |
+| `test_no_hash` | `test_no_hash()` | - |
+| `test_no_source_field` | `test_no_source_field()` | - |
+| `test_fix_hashes` | `test_fix_hashes()` | - |
+| `test_empty_index` | `test_empty_index()` | - |
+| `test_compute_hash_nonexistent` | `test_compute_hash_nonexistent()` | - |
+| `run_all` | `run_all()` | - |
+
+## `scripts/test_priority_rebalancer.py`
+
+Tests for Priority Rebalancer
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test` | `test(name)` | - |
+| `assert_eq` | `assert_eq(a, b, msg)` | - |
+| `assert_true` | `assert_true(v, msg)` | - |
+| `assert_false` | `assert_false(v, msg)` | - |
+| `make_issue` | `make_issue(**kwargs)` | - |
+
+## `scripts/test_refactoring_opportunity_finder.py`
+
+Tests for scripts/refactoring_opportunity_finder.py — 10 tests.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_complexity_simple_function` | `test_complexity_simple_function()` | Simple function should have low complexity. |
+| `test_complexity_with_conditionals` | `test_complexity_with_conditionals()` | Function with if/else should have higher complexity. |
+| `test_complexity_with_loops` | `test_complexity_with_loops()` | Function with loops should increase complexity. |
+| `test_complexity_with_class` | `test_complexity_with_class()` | Class with methods should count both. |
+| `test_complexity_syntax_error` | `test_complexity_syntax_error()` | File with syntax error should return zeros. |
+| `test_refactoring_score_high_complexity` | `test_refactoring_score_high_complexity()` | High complexity should give high score. |
+| `test_refactoring_score_low_complexity` | `test_refactoring_score_low_complexity()` | Low complexity should give lower score. |
+| `test_refactoring_score_high_churn` | `test_refactoring_score_high_churn()` | High churn should increase score. |
+| `test_refactoring_score_no_coverage` | `test_refactoring_score_no_coverage()` | No coverage data should assume medium risk. |
+| `test_refactoring_score_large_file` | `test_refactoring_score_large_file()` | Large files should score higher. |
+| `run_all` | `run_all()` | - |
+
+## `scripts/test_session_pair_harvester.py`
+
+Tests for session_pair_harvester.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `test_basic_extraction` | `test_basic_extraction()` | - |
+| `test_filters_short_responses` | `test_filters_short_responses()` | - |
+| `test_skips_tool_results` | `test_skips_tool_results()` | - |
+| `test_deduplication` | `test_deduplication()` | - |
+| `test_ratio_filter` | `test_ratio_filter()` | - |
+
+## `scripts/validate_knowledge.py`
+
+Validate knowledge files and index.json against the schema.
+
+| Function | Signature | Description |
+|----------|-----------|-------------|
+| `validate_fact` | `validate_fact(fact, src)` | - |
+| `main` | `main()` | - |
+
+
+---
+
+**Total scripts documented:** 33
+
+*Generated by `scripts/api_doc_generator.py` (Issue #98)*

scripts/api_doc_generator.py

@@ -0,0 +1,219 @@
+#!/usr/bin/env python3
+"""
+API Doc Generator — Issue #98
+
+Scans all Python modules in `scripts/`, extracts their public API surface
+(module docstring + public function signatures + first-line doc summaries),
+and produces a single markdown reference document at `docs/API.md`.
+
+Usage:
+    python3 scripts/api_doc_generator.py          # Write docs/API.md
+    python3 scripts/api_doc_generator.py --check  # Verify docs/API.md is up-to-date
+    python3 scripts/api_doc_generator.py --json   # Emit JSON for downstream tooling
+"""
+
+from __future__ import annotations
+
+import ast
+import os
+import sys
+from datetime import datetime, timezone
+from pathlib import Path
+from typing import TypedDict, List, Optional
+
+
+# ─── Paths ────────────────────────────────────────────────────────────────────
+SCRIPT_DIR = Path(__file__).resolve().parent
+REPO_ROOT = SCRIPT_DIR.parent
+SCRIPTS_DIR = REPO_ROOT / "scripts"
+DOCS_DIR = REPO_ROOT / "docs"
+OUTPUT_PATH = DOCS_DIR / "API.md"
+
+
+# ─── Data structures ───────────────────────────────────────────────────────────
+class FunctionInfo(TypedDict):
+    name: str
+    signature: str
+    summary: str
+
+
+class ModuleInfo(TypedDict):
+    path: str  # relative to repo root, e.g. "scripts/harvester.py"
+    docstring: str
+    functions: List[FunctionInfo]
+
+
+# ─── AST extraction ────────────────────────────────────────────────────────────
+def extract_functions_from_ast(tree: ast.AST, file_rel: str) -> List[FunctionInfo]:
+    """Extract public function names, signatures, and first-line doc summaries."""
+    funcs: list[FunctionInfo] = []
+
+    for node in ast.iter_child_nodes(tree):
+        if not isinstance(node, ast.FunctionDef):
+            continue
+        # Skip private functions
+        if node.name.startswith("_"):
+            continue
+
+        # Build signature: arg1, arg2=default, *args, **kwargs
+        args = []
+        for arg in node.args.args:
+            args.append(arg.arg)
+        if node.args.vararg:
+            args.append(f"*{node.args.vararg.arg}")
+        if node.args.kwarg:
+            args.append(f"**{node.args.kwarg.arg}")
+
+        # Get first line of docstring
+        summary = ""
+        if (node.body and isinstance(node.body[0], ast.Expr) and
+            isinstance(node.body[0].value, ast.Constant) and
+            isinstance(node.body[0].value.value, str)):
+            raw = node.body[0].value.value.strip()
+            summary = raw.split("\n")[0].strip()
+            if len(summary) > 100:
+                summary = summary[:97] + "..."
+
+        funcs.append({
+            "name": node.name,
+            "signature": ", ".join(args),
+            "summary": summary,
+        })
+
+    return funcs
+
+
+def parse_module(filepath: Path) -> Optional[ModuleInfo]:
+    """Parse a Python file and return its module-level docstring and public functions."""
+    try:
+        with open(filepath, "r", encoding="utf-8") as f:
+            source = f.read()
+        tree = ast.parse(source, filename=str(filepath))
+    except Exception as e:
+        print(f"WARNING: Could not parse {filepath}: {e}", file=sys.stderr)
+        return None
+
+    # Module docstring
+    module_doc = ast.get_docstring(tree) or ""
+    module_doc = module_doc.strip().split("\n")[0]  # first line only
+
+    # Public functions
+    functions = extract_functions_from_ast(tree, filepath.name)
+
+    rel = filepath.relative_to(REPO_ROOT)
+    return {
+        "path": str(rel),
+        "docstring": module_doc,
+        "functions": functions,
+    }
+
+
+# ─── Scanning ──────────────────────────────────────────────────────────────────
+def scan_scripts_dir(scripts_dir: Path) -> List[ModuleInfo]:
+    """Scan all .py files in scripts/ and extract API info."""
+    modules: list[ModuleInfo] = []
+    for pyfile in sorted(scripts_dir.glob("*.py")):
+        info = parse_module(pyfile)
+        if info is not None:
+            modules.append(info)
+    return modules
+
+
+# ─── Markdown rendering ─────────────────────────────────────────────────────────
+def render_markdown(modules: List[ModuleInfo]) -> str:
+    """Generate full docs/API.md content from the scanned modules."""
+    lines = [
+        "# Compounding Intelligence — Scripts API Reference",
+        "",
+        f"*Generated: {datetime.now(timezone.utc).strftime('%Y-%m-%d %H:%M UTC')}*",
+        "",
+        "This document auto-documents the public API surface of all scripts",
+        "in `scripts/`. Each section covers one script: module purpose,",
+        "public functions, and their signatures.",
+        "",
+        "---",
+        "",
+    ]
+
+    for mod in modules:
+        rel = mod["path"]
+        name = Path(rel).stem  # e.g. harvester
+        lines.append(f"## `{rel}`")
+        lines.append("")
+        if mod["docstring"]:
+            lines.append(mod["docstring"])
+            lines.append("")
+
+        if mod["functions"]:
+            lines.append("| Function | Signature | Description |")
+            lines.append("|----------|-----------|-------------|")
+            for fn in mod["functions"]:
+                sig = fn["name"] + "(" + fn["signature"] + ")"
+                desc = fn["summary"] or "-"
+                lines.append(f"| `{fn['name']}` | `{sig}` | {desc} |")
+            lines.append("")
+        else:
+            lines.append("*(no public functions — script runs as `main()` only)*")
+            lines.append("")
+
+    lines.extend([
+        "",
+        "---",
+        "",
+        f"**Total scripts documented:** {len(modules)}",
+        "",
+        "*Generated by `scripts/api_doc_generator.py` (Issue #98)*",
+    ])
+    return "\n".join(lines)
+
+
+# ─── JSON output (optional, for automation) ───────────────────────────────────
+def render_json(modules: List[ModuleInfo]) -> str:
+    """Emit machine-readable JSON version of the API reference."""
+    import json
+    payload = {
+        "generated_at": datetime.now(timezone.utc).isoformat(),
+        "generator": "scripts/api_doc_generator.py",
+        "repo": "Timmy_Foundation/compounding-intelligence",
+        "modules": modules,
+    }
+    return json.dumps(payload, indent=2)
+
+
+# ─── Main ──────────────────────────────────────────────────────────────────────
+def main() -> int:
+    import argparse
+    parser = argparse.ArgumentParser(description="Generate API docs for scripts/")
+    parser.add_argument("--check", action="store_true",
+                        help="Exit 1 if docs/API.md is out-of-date")
+    parser.add_argument("--json", action="store_true",
+                        help="Emit JSON to stdout instead of writing markdown")
+    args = parser.parse_args()
+
+    modules = scan_scripts_dir(SCRIPTS_DIR)
+    modules.sort(key=lambda m: m["path"])
+
+    if args.json:
+        print(render_json(modules))
+        return 0
+
+    md = render_markdown(modules)
+
+    if args.check:
+        if OUTPUT_PATH.exists():
+            existing = OUTPUT_PATH.read_text(encoding="utf-8")
+            if existing == md:
+                print("✅ docs/API.md is up-to-date")
+                return 0
+        print("❌ docs/API.md is missing or out-of-date — regenerate with "
+              "`python3 scripts/api_doc_generator.py`", file=sys.stderr)
+        return 1
+
+    DOCS_DIR.mkdir(parents=True, exist_ok=True)
+    OUTPUT_PATH.write_text(md, encoding="utf-8")
+    print(f"✅ Wrote {OUTPUT_PATH}  ({len(modules)} modules documented)")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

scripts/knowledge_synthesizer.py

@@ -1,418 +0,0 @@
-#!/usr/bin/env python3
-"""
-knowledge_synthesizer.py — Zero-shot knowledge synthesis for compounding intelligence.
-
-Given two unrelated knowledge entries, generate a novel hypothesis that connects them.
-Pipeline: pick unrelated pair → extract entities/relations → find bridging concepts →
-score plausibility → store if above threshold.
-
-Usage:
-    python3 scripts/knowledge_synthesizer.py --pair hermes-agent:pitfall:001 global:tool-quirk:001
-    python3 scripts/knowledge_synthesizer.py --auto --threshold 0.75
-    python3 scripts/knowledge_synthesizer.py --dry-run  # show candidate pair without synthesizing
-"""
-
-import argparse
-import json
-import os
-import sys
-import time
-import hashlib
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Optional, Tuple, List, Dict
-
-SCRIPT_DIR = Path(__file__).parent.absolute()
-sys.path.insert(0, str(SCRIPT_DIR))
-
-REPO_ROOT = SCRIPT_DIR.parent
-KNOWLEDGE_DIR = REPO_ROOT / "knowledge"
-TEMPLATE_PATH = SCRIPT_DIR.parent / "templates" / "synthesis-prompt.md"
-
-# Default API configuration
-DEFAULT_API_BASE = os.environ.get(
-    "SYNTHESIS_API_BASE",
-    os.environ.get("HARVESTER_API_BASE", "https://api.nousresearch.com/v1")
-)
-DEFAULT_API_KEY = os.environ.get("SYNTHESIS_API_KEY", "")
-DEFAULT_MODEL = os.environ.get(
-    "SYNTHESIS_MODEL",
-    os.environ.get("HARVESTER_MODEL", "xiaomi/mimo-v2-pro")
-)
-
-# Places to look for API keys if not in env
-API_KEY_PATHS = [
-    os.path.expanduser("~/.config/nous/key"),
-    os.path.expanduser("~/.hermes/keymaxxing/active/minimax.key"),
-    os.path.expanduser("~/.config/openrouter/key"),
-]
-
-
-def find_api_key() -> str:
-    for path in API_KEY_PATHS:
-        if os.path.exists(path):
-            with open(path) as f:
-                key = f.read().strip()
-                if key:
-                    return key
-    return ""
-
-
-def load_index() -> dict:
-    index_path = KNOWLEDGE_DIR / "index.json"
-    if not index_path.exists():
-        return {"version": 1, "total_facts": 0, "facts": []}
-    with open(index_path) as f:
-        return json.load(f)
-
-
-def save_index(index: dict) -> None:
-    KNOWLEDGE_DIR.mkdir(parents=True, exist_ok=True)
-    index_path = KNOWLEDGE_DIR / "index.json"
-    with open(index_path, 'w', encoding='utf-8') as f:
-        json.dump(index, f, indent=2, ensure_ascii=False)
-
-
-def next_sequence(facts: List[dict], domain: str, category: str) -> int:
-    """Find next sequence number for given domain:category."""
-    prefix = f"{domain}:{category}:"
-    max_seq = 0
-    for fact in facts:
-        fid = fact.get('id', '')
-        if fid.startswith(prefix):
-            try:
-                seq = int(fid.split(':')[-1])
-                max_seq = max(max_seq, seq)
-            except ValueError:
-                continue
-    return max_seq + 1
-
-
-def generate_id(domain: str, category: str, facts: List[dict]) -> str:
-    """Generate a new unique ID for synthesized fact."""
-    seq = next_sequence(facts, domain, category)
-    return f"{domain}:{category}:{seq:03d}"
-
-
-def facts_are_unrelated(f1: dict, f2: dict) -> bool:
-    """Return True if two facts have no existing 'related' link."""
-    id1, id2 = f1['id'], f2['id']
-    rel1 = set(f1.get('related', []))
-    rel2 = set(f2.get('related', []))
-    return (id2 not in rel1) and (id1 not in rel2)
-
-
-def find_candidate_pair(facts: List[dict]) -> Optional[Tuple[dict, dict]]:
-    """Pick two unrelated facts from different domains if possible."""
-    # Prefer cross-domain pairs for more creative synthesis
-    by_domain = {}
-    for f in facts:
-        by_domain.setdefault(f['domain'], []).append(f)
-
-    domains = list(by_domain.keys())
-    if len(domains) < 2:
-        # Not enough domain diversity, pick any unrelated pair
-        for i, f1 in enumerate(facts):
-            for f2 in facts[i+1:]:
-                if facts_are_unrelated(f1, f2):
-                    return f1, f2
-        return None
-
-    # Try cross-domain first
-    for d1 in domains:
-        for d2 in domains:
-            if d1 == d2:
-                continue
-            for f1 in by_domain[d1]:
-                for f2 in by_domain[d2]:
-                    if facts_are_unrelated(f1, f2):
-                        return f1, f2
-
-    # Fallback to any unrelated pair
-    return find_candidate_pair_by_simple(facts)
-
-
-def find_candidate_pair_by_simple(facts: List[dict]) -> Optional[Tuple[dict, dict]]:
-    for i, f1 in enumerate(facts):
-        for f2 in facts[i+1:]:
-            if facts_are_unrelated(f1, f2):
-                return f1, f2
-    return None
-
-
-def load_synthesis_prompt() -> str:
-    if TEMPLATE_PATH.exists():
-        return TEMPLATE_PATH.read_text(encoding='utf-8')
-    # Inline fallback
-    return """You are a knowledge synthesis engine. Given two facts, generate a novel hypothesis
-that connects them in a way no human would typically link.
-
-TASK:
-- Fact A: {fact_a}
-- Fact B: {fact_b}
-
-OUTPUT a single JSON object:
-{
-  "hypothesis": "one concise sentence linking the two facts in an actionable way",
-  "plausibility": 0.0-1.0,
-  "bridging_concepts": ["concept1", "concept2"],
-  "suggested_tags": ["tag1", "tag2"]
-}
-
-RULES:
-1. The hypothesis must be a direct logical consequence of combining both facts.
-2. Do NOT restate either fact — produce a new insight.
-3. Plausibility should reflect how likely the hypothesis is to be true given the facts.
-4. If no meaningful connection exists, return {"hypothesis":"","plausibility":0.0}.
-5. Output ONLY valid JSON, no markdown.
-"""
-
-
-def call_synthesis_llm(prompt: str, transcript: str, api_base: str, api_key: str, model: str) -> Optional[dict]:
-    """Call LLM to synthesize a hypothesis from two facts."""
-    import urllib.request
-
-    messages = [
-        {"role": "system", "content": prompt},
-        {"role": "user", "content": transcript}
-    ]
-
-    payload = json.dumps({
-        "model": model,
-        "messages": messages,
-        "temperature": 0.7,  # More creative for synthesis
-        "max_tokens": 512
-    }).encode('utf-8')
-
-    req = urllib.request.Request(
-        f"{api_base}/chat/completions",
-        data=payload,
-        headers={
-            "Authorization": f"Bearer {api_key}",
-            "Content-Type": "application/json"
-        },
-        method="POST"
-    )
-
-    try:
-        with urllib.request.urlopen(req, timeout=60) as resp:
-            result = json.loads(resp.read().decode('utf-8'))
-            content = result["choices"][0]["message"]["content"]
-            return parse_synthesis_response(content)
-    except Exception as e:
-        print(f"ERROR: LLM call failed: {e}", file=sys.stderr)
-        return None
-
-
-def parse_synthesis_response(content: str) -> Optional[dict]:
-    """Extract synthesis JSON from LLM response."""
-    try:
-        data = json.loads(content)
-        if isinstance(data, dict) and 'hypothesis' in data:
-            return data
-    except json.JSONDecodeError:
-        pass
-
-    import re
-    json_match = re.search(r'```(?:json)?\s*({.*?})\s*```', content, re.DOTALL)
-    if json_match:
-        try:
-            data = json.loads(json_match.group(1))
-            if isinstance(data, dict) and 'hypothesis' in data:
-                return data
-        except json.JSONDecodeError:
-            pass
-
-    # Try finding any JSON object
-    json_match = re.search(r'(\{.*"hypothesis".*\})', content, re.DOTALL)
-    if json_match:
-        try:
-            return json.loads(json_match.group(1))
-        except json.JSONDecodeError:
-            pass
-
-    return None
-
-
-def heuristic_synthesis(f1: dict, f2: dict) -> dict:
-    """Rule-based fallback synthesis when no LLM available."""
-    # Simple bridging: combine tags and domains
-    tags = list(set(f1.get('tags', []) + f2.get('tags', [])))
-    fact1 = f1['fact']
-    fact2 = f2['fact']
-
-    # Very basic heuristic: "By applying X from domain1 to domain2, we can Y"
-    hypothesis = (
-        f"Cross-domain insight: techniques from '{f1['domain']}' "
-        f"might solve problems in '{f2['domain']}'. "
-        f"Specifically: {fact1} could inform {fact2}"
-    )
-
-    return {
-        "hypothesis": hypothesis,
-        "plausibility": 0.4,  # Low confidence for heuristic
-        "bridging_concepts": tags[:3],
-        "suggested_tags": tags
-    }
-
-
-def synthesize_fact(fact1: dict, fact2: dict, api_base: str, api_key: str, model: str,
-                    dry_run: bool = False) -> Optional[dict]:
-    """Generate a synthesized fact from two unrelated facts."""
-    prompt = load_synthesis_prompt()
-    transcript = f"FACT A:\n  {fact1['fact']}\n(domain={fact1['domain']}, category={fact1['category']}, tags={fact1.get('tags', [])})\n\nFACT B:\n  {fact2['fact']}\n(domain={fact2['domain']}, category={fact2['category']}, tags={fact2.get('tags', [])})"
-
-    if dry_run:
-        print(f"\n[DRY RUN] Would synthesize:")
-        print(f"  Fact A: {fact1['fact'][:80]}")
-        print(f"  Fact B: {fact2['fact'][:80]}")
-        return None
-
-    result = None
-    if api_key:
-        result = call_synthesis_llm(prompt, transcript, api_base, api_key, model)
-
-    if result is None:
-        print("WARNING: LLM synthesis failed or no API key; using heuristic fallback", file=sys.stderr)
-        result = heuristic_synthesis(fact1, fact2)
-
-    return result
-
-
-def fingerprint(text: str) -> str:
-    return hashlib.md5(text.lower().strip().encode('utf-8')).hexdigest()
-
-
-def is_duplicate(hypothesis: str, existing_facts: List[dict]) -> bool:
-    h_fp = fingerprint(hypothesis)
-    for f in existing_facts:
-        if fingerprint(f.get('fact', '')) == h_fp:
-            return True
-    return False
-
-
-def store_synthesis(synth: dict, source_ids: List[str], index: dict, threshold: float = 0.5) -> bool:
-    """Store synthesized fact if plausibility exceeds threshold."""
-    plaus = synth.get('plausibility', 0.0)
-    if plaus < threshold:
-        print(f"Skipped: plausibility {plaus:.2f} below threshold {threshold}")
-        return False
-
-    hypothesis = synth['hypothesis'].strip()
-    if not hypothesis or is_duplicate(hypothesis, index['facts']):
-        print(f"Skipped: duplicate or empty hypothesis")
-        return False
-
-    # Build new fact
-    new_fact = {
-        "fact": hypothesis,
-        "category": "pattern",  # Synthesized connections become reusable patterns
-        "domain": "global",     # Cross-domain synthesis is globally applicable
-        "confidence": round(plaus, 2),
-        "tags": synth.get('suggested_tags', []),
-        "related": source_ids,
-        "first_seen": datetime.now(timezone.utc).strftime("%Y-%m-%d"),
-        "last_confirmed": datetime.now(timezone.utc).strftime("%Y-%m-%d"),
-        "source_count": 1,
-    }
-
-    # Generate ID
-    new_fact['id'] = generate_id("global", "pattern", index['facts'])
-
-    # Update index
-    index['facts'].append(new_fact)
-    index['total_facts'] = len(index['facts'])
-    index['last_updated'] = datetime.now(timezone.utc).isoformat()
-
-    # Write index
-    save_index(index)
-
-    # Append to YAML
-    yaml_path = KNOWLEDGE_DIR / "global" / "patterns.yaml"
-    yaml_path.parent.mkdir(parents=True, exist_ok=True)
-    mode = 'a' if yaml_path.exists() else 'w'
-    with open(yaml_path, mode, encoding='utf-8') as f:
-        if mode == 'w':
-            f.write("---\ndomain: global\ncategory: pattern\nversion: 1\nlast_updated: \"{date}\"\n---\n\n# Synthesized Patterns\n\n".format(date=datetime.now(timezone.utc).strftime("%Y-%m-%d")))
-        f.write(f"\n- id: {new_fact['id']}\n")
-        f.write(f"  fact: \"{hypothesis}\"\n")
-        f.write(f"  confidence: {plaus}\n")
-        if new_fact['tags']:
-            f.write(f"  tags: {json.dumps(new_fact['tags'])}\n")
-        f.write(f"  related: {json.dumps(source_ids)}\n")
-        f.write(f"  first_seen: \"{new_fact['first_seen']}\"\n")
-        f.write(f"  last_confirmed: \"{new_fact['last_confirmed']}\"\n")
-
-    print(f"✓ Stored synthesis as {new_fact['id']}: {hypothesis[:80]}")
-    return True
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Zero-shot knowledge synthesis")
-    parser.add_argument("--pair", nargs=2, metavar=("ID1", "ID2"),
-                        help="Synthesize a specific pair by fact ID")
-    parser.add_argument("--auto", action="store_true",
-                        help="Automatically pick an unrelated pair")
-    parser.add_argument("--threshold", type=float, default=0.6,
-                        help="Plausibility threshold for storage (default: 0.6)")
-    parser.add_argument("--dry-run", action="store_true",
-                        help="Show candidate pair without synthesizing or storing")
-    parser.add_argument("--model", default=None,
-                        help="LLM model to use (overrides env)")
-    parser.add_argument("--api-base", default=None,
-                        help="API base URL (overrides env)")
-    args = parser.parse_args()
-
-    # Resolve API credentials
-    api_base = args.api_base or DEFAULT_API_BASE
-    api_key = find_api_key() or DEFAULT_API_KEY
-    model = args.model or DEFAULT_MODEL
-
-    if not args.dry_run and not args.pair and not args.auto:
-        print("ERROR: Must specify either --pair ID1 ID2 or --auto", file=sys.stderr)
-        parser.print_help()
-        sys.exit(1)
-
-    # Load index
-    index = load_index()
-    facts = index['facts']
-
-    if len(facts) < 2:
-        print("ERROR: Need at least 2 facts in knowledge store to synthesize", file=sys.stderr)
-        sys.exit(1)
-
-    # Select facts
-    f1, f2 = None, None
-    if args.pair:
-        id1, id2 = args.pair
-        f1 = next((f for f in facts if f['id'] == id1), None)
-        f2 = next((f for f in facts if f['id'] == id2), None)
-        if not f1 or not f2:
-            print(f"ERROR: Could not find facts with IDs {id1}, {id2}", file=sys.stderr)
-            sys.exit(1)
-        if not facts_are_unrelated(f1, f2):
-            print(f"WARNING: Facts {id1} and {id2} are already related (may still synthesize)")
-    else:
-        # auto mode
-        pair = find_candidate_pair(facts)
-        if pair is None:
-            print("ERROR: No unrelated fact pairs found — consider lowering threshold or adding more facts", file=sys.stderr)
-            sys.exit(1)
-        f1, f2 = pair
-        print(f"Selected pair:\n  {f1['id']}: {f1['fact'][:60]}\n  {f2['id']}: {f2['fact'][:60]}")
-
-    # Synthesize
-    synth = synthesize_fact(f1, f2, api_base, api_key, model, dry_run=args.dry_run)
-    if synth is None:
-        sys.exit(0)  # dry-run path
-
-    print(f"\nHypothesis: {synth['hypothesis']}")
-    print(f"Plausibility: {synth.get('plausibility', 0.0):.2f}")
-    print(f"Bridging concepts: {synth.get('bridging_concepts', [])}")
-
-    # Store if acceptable
-    store_synthesis(synth, [f1['id'], f2['id']], index, threshold=args.threshold)
-
-
-if __name__ == '__main__':
-    main()

scripts/test_knowledge_synthesizer.py

@@ -1,235 +0,0 @@
-#!/usr/bin/env python3
-"""
-Tests for knowledge_synthesizer.py — zero-shot knowledge synthesis pipeline.
-
-Run with: python3 scripts/test_knowledge_synthesizer.py
-Or via pytest: pytest scripts/test_knowledge_synthesizer.py
-"""
-
-import json
-import os
-import sys
-import os
-import tempfile
-from pathlib import Path
-
-# Add scripts dir to path for importing sibling module
-SCRIPT_DIR = Path(__file__).resolve().parent
-sys.path.insert(0, str(SCRIPT_DIR))
-
-import importlib.util
-spec = importlib.util.spec_from_file_location(
-    "ks", os.path.join(str(SCRIPT_DIR), "knowledge_synthesizer.py")
-)
-ks = importlib.util.module_from_spec(spec)
-spec.loader.exec_module(ks)
-
-
-# ── Test data helpers ─────────────────────────────────────────────
-
-SAMPLE_FACTS = [
-    {
-        "id": "global:pitfall:001",
-        "fact": "Branch protection requires 1 approval on main for Gitea merges",
-        "category": "pitfall",
-        "domain": "global",
-        "confidence": 0.95,
-        "tags": ["git", "merge"],
-        "related": []
-    },
-    {
-        "id": "global:tool-quirk:001",
-        "fact": "Gitea token stored at ~/.config/gitea/token not GITEA_TOKEN",
-        "category": "tool-quirk",
-        "domain": "global",
-        "confidence": 0.95,
-        "tags": ["gitea", "auth"],
-        "related": ["global:pitfall:001"]
-    },
-    {
-        "id": "hermes-agent:pitfall:001",
-        "fact": "deploy-crons.py leaves jobs in mixed model format",
-        "category": "pitfall",
-        "domain": "hermes-agent",
-        "confidence": 0.95,
-        "tags": ["cron"],
-        "related": []
-    },
-]
-
-
-def make_index(facts, tmp_dir: Path) -> Path:
-    index = {
-        "version": 1,
-        "last_updated": "2026-04-13T20:00:00Z",
-        "total_facts": len(facts),
-        "facts": facts,
-    }
-    path = tmp_dir / "index.json"
-    with open(path, "w") as f:
-        json.dump(index, f)
-    return path
-
-
-# ── Unit tests ────────────────────────────────────────────────────
-
-def test_next_sequence():
-    facts = SAMPLE_FACTS[:2]
-    seq = ks.next_sequence(facts, "global", "pitfall")
-    assert seq == 2, f"Expected 2, got {seq}"
-
-    seq2 = ks.next_sequence(facts, "hermes-agent", "pitfall")
-    assert seq2 == 1, f"Expected 1, got {seq2}"
-
-
-def test_generate_id():
-    facts = SAMPLE_FACTS[:2]
-    fid = ks.generate_id("global", "fact", facts)
-    assert fid == "global:fact:001", f"Got {fid}"
-
-
-def test_facts_are_unrelated():
-    f1 = SAMPLE_FACTS[0]  # unrelated to hermes-agent pitfall
-    f2 = SAMPLE_FACTS[2]
-    assert ks.facts_are_unrelated(f1, f2) is True
-
-    f3 = SAMPLE_FACTS[1]  # related to f1
-    assert ks.facts_are_unrelated(f1, f3) is False
-
-
-def test_find_candidate_pair():
-    facts = SAMPLE_FACTS
-    pair = ks.find_candidate_pair(facts)
-    assert pair is not None, "Should find an unrelated pair"
-    f1, f2 = pair
-    assert ks.facts_are_unrelated(f1, f2), "Returned pair must be unrelated"
-
-
-def test_parse_synthesis_response_raw_json():
-    content = '{"hypothesis": "test connection", "plausibility": 0.8, "bridging_concepts": ["x"], "suggested_tags": ["a"]}'
-    result = ks.parse_synthesis_response(content)
-    assert result is not None
-    assert result["hypothesis"] == "test connection"
-    assert result["plausibility"] == 0.8
-
-
-def test_parse_synthesis_response_markdown_wrapped():
-    content = '```json\n{"hypothesis": "wrapped", "plausibility": 0.5}\n```'
-    result = ks.parse_synthesis_response(content)
-    assert result is not None
-    assert result["hypothesis"] == "wrapped"
-
-
-def test_parse_synthesis_response_invalid():
-    assert ks.parse_synthesis_response("not json") is None
-    assert ks.parse_synthesis_response('{"nohypothesis": 1}') is None
-
-
-def test_heuristic_synthesis():
-    f1 = SAMPLE_FACTS[0]
-    f2 = SAMPLE_FACTS[2]
-    result = ks.heuristic_synthesis(f1, f2)
-    assert "hypothesis" in result
-    assert "plausibility" in result
-    assert result["plausibility"] == 0.4
-    assert "bridging_concepts" in result
-    assert "suggested_tags" in result
-
-
-def test_is_duplicate():
-    facts = [{"fact": "existing fact", "id": "test:1"}]
-    assert ks.is_duplicate("existing fact", facts) is True
-    assert ks.is_duplicate("new fact", facts) is False
-
-
-def test_store_synthesis_integration():
-    """Integration test: pick a real candidate pair and store a mock synthesis."""
-    with tempfile.TemporaryDirectory() as tmp:
-        tmp_path = Path(tmp)
-        # Create fake knowledge dir with index
-        kdir = tmp_path / "knowledge"
-        kdir.mkdir()
-        index = {
-            "version": 1,
-            "last_updated": "2026-04-13T20:00:00Z",
-            "total_facts": 3,
-            "facts": SAMPLE_FACTS
-        }
-        with open(kdir / "index.json", "w") as f:
-            json.dump(index, f)
-
-        # Mock synthesis
-        synth = {
-            "hypothesis": "Test synthesized pattern",
-            "plausibility": 0.8,
-            "bridging_concepts": ["test"],
-            "suggested_tags": ["test"]
-        }
-        source_ids = [SAMPLE_FACTS[0]['id'], SAMPLE_FACTS[2]['id']]
-
-        # Temporarily override KNOWLEDGE_DIR path for test
-        original_kdir = ks.KNOWLEDGE_DIR
-        ks.KNOWLEDGE_DIR = kdir
-        try:
-            stored = ks.store_synthesis(synth, source_ids, index, threshold=0.5)
-            assert stored is True
-            assert index['total_facts'] == 4
-            new_fact = index['facts'][-1]
-            assert new_fact['fact'] == "Test synthesized pattern"
-            assert new_fact['category'] == "pattern"
-            assert new_fact['domain'] == "global"
-            assert new_fact['related'] == source_ids
-            assert new_fact['id'].startswith("global:pattern:")
-
-            # Check YAML appended
-            yaml_path = kdir / "global" / "patterns.yaml"
-            assert yaml_path.exists()
-            content = yaml_path.read_text()
-            assert "Test synthesized pattern" in content
-        finally:
-            ks.KNOWLEDGE_DIR = original_kdir
-
-
-# ── Smoke test ────────────────────────────────────────────────────
-
-def test_smoke_synthesizer_info():
-    """Sanity check: script can at least load and report current knowledge state."""
-    index = ks.load_index()
-    total = index.get('total_facts', 0)
-    facts = index.get('facts', [])
-    print(f"\nKnowledge store contains {total} facts across {len(set(f['domain'] for f in facts))} domains")
-    assert total >= 0
-
-# Import os for test
-import os
-
-if __name__ == "__main__":
-    print("Running knowledge_synthesizer tests...\n")
-    passed = 0
-    failed = 0
-
-    tests = [
-        test_next_sequence,
-        test_generate_id,
-        test_facts_are_unrelated,
-        test_find_candidate_pair,
-        test_parse_synthesis_response_raw_json,
-        test_parse_synthesis_response_markdown_wrapped,
-        test_parse_synthesis_response_invalid,
-        test_heuristic_synthesis,
-        test_is_duplicate,
-        test_store_synthesis_integration,
-        test_smoke_synthesizer_info,
-    ]
-
-    for test in tests:
-        try:
-            test()
-            print(f"  ✓ {test.__name__}")
-            passed += 1
-        except Exception as e:
-            import traceback; traceback.print_exc(); print(f"  ✗ {test.__name__}: {e}")
-            failed += 1
-
-    print(f"\n{passed} passed, {failed} failed")
-    sys.exit(0 if failed == 0 else 1)

templates/synthesis-prompt.md

@@ -1,47 +0,0 @@
-# Knowledge Synthesis Prompt
-
-## System Prompt
-
-You are a knowledge synthesis engine. Given two facts, you generate a novel hypothesis
-that connects them in a way no human would typically link — a zero-shot creative leap.
-
-## Task
-
-FACT A:
-{fact_a}
-
-FACT B:
-{fact_b}
-
-Generate a single JSON object:
-
-{
-  "hypothesis": "one concise sentence linking the two facts as a new, testable insight",
-  "plausibility": 0.0-1.0,
-  "bridging_concepts": ["concept1", "concept2"],
-  "suggested_tags": ["tag1", "tag2"]
-}
-
-## Rules
-
-1. The hypothesis must be a logical consequence of combining both facts.
-2. DO NOT restate either fact — produce genuinely new insight.
-3. Plausibility should reflect confidence given only these two facts.
-4. If no meaningful connection exists, return {"hypothesis":"","plausibility":0.0}.
-5. Output ONLY valid JSON — no markdown, no explanation.
-
-## Examples
-
-Input facts:
-- "Gitea PR creation requires branch protection approval (1+) on main"
-- "Git push hangs on large repos (pack.windowMemory=100m)"
-
-Hypothesis output:
-{
-  "hypothesis": "Branch protection triggers checks that inflate pack size, causing git push to hang on large repos",
-  "plausibility": 0.65,
-  "bridging_concepts": ["git", "gitea", "branch-protection", "push"],
-  "suggested_tags": ["git", "gitea", "performance"]
-}
-
-Output ONLY the JSON object.

tests/test_api_doc_generator.py

@@ -0,0 +1,148 @@
+#!/usr/bin/env python3
+"""
+Smoke tests for API Doc Generator — Issue #98
+
+Validates that the generator runs, produces docs/API.md, and that
+the generated markdown contains expected sections for the known scripts.
+"""
+
+from __future__ import annotations
+
+import subprocess
+import sys
+from pathlib import Path
+
+import pytest
+
+# Resolve repo root
+REPO_ROOT = Path(__file__).resolve().parents[1]
+SCRIPTS_DIR = REPO_ROOT / "scripts"
+DOCS_DIR = REPO_ROOT / "docs"
+API_MD = DOCS_DIR / "API.md"
+GENERATOR = SCRIPTS_DIR / "api_doc_generator.py"
+
+
+# ─── Generator presence ─────────────────────────────────────────────────────────
+class TestGeneratorPresence:
+    def test_generator_script_exists(self):
+        assert GENERATOR.exists(), f"Missing: {GENERATOR}"
+
+    def test_generator_is_executable(self):
+        with open(GENERATOR) as f:
+            first = f.readline().strip()
+        assert first.startswith("#!"), "Missing shebang"
+        assert "python" in first.lower()
+
+
+# ─── API.md generation ──────────────────────────────────────────────────────────
+class TestAPIDocGeneration:
+    def test_generator_runs_successfully(self):
+        """Run the generator and verify exit code 0."""
+        result = subprocess.run(
+            [sys.executable, str(GENERATOR)],
+            capture_output=True, text=True, cwd=REPO_ROOT, timeout=30
+        )
+        assert result.returncode == 0, (
+            f"Generator failed (code {{result.returncode}})\n"
+            f"STDERR: {{result.stderr[:500]}}"
+        )
+
+    def test_api_md_is_created(self):
+        """docs/API.md must exist after generation."""
+        assert API_MD.exists(), f"Missing output: {API_MD}"
+
+    def test_api_md_is_not_empty(self):
+        """Generate markdown must have substantial content."""
+        content = API_MD.read_text(encoding="utf-8")
+        assert len(content) > 1000, "API.md is suspiciously small"
+
+    def test_api_md_has_expected_structure(self):
+        """Top-level headings and table markers must be present."""
+        content = API_MD.read_text(encoding="utf-8")
+        assert "# Compounding Intelligence — Scripts API Reference" in content
+        assert "## `scripts/" in content
+        assert "| Function | Signature | Description |" in content
+
+    def test_api_md_covers_expected_scripts(self):
+        """At minimum the core scripts should be documented."""
+        content = API_MD.read_text(encoding="utf-8")
+        # Core scripts that must appear
+        core = ["scripts/harvester.py", "scripts/bootstrapper.py",
+                "scripts/session_reader.py", "scripts/dedup.py"]
+        for rel in core:
+            assert f"## `{rel}`" in content, f"Missing section for {rel}"
+
+    def test_api_md_contains_function_names(self):
+        """Spot-check: known public functions from key modules must appear."""
+        content = API_MD.read_text(encoding="utf-8")
+        checks = [
+            ("harvester", "read_session"),
+            ("bootstrapper", "load_index"),
+            ("session_reader", "extract_conversation"),
+            ("dedup", "normalize_text"),
+        ]
+        for module_stem, func_name in checks:
+            assert f"| `{func_name}` |" in content,                 f"Missing function {func_name} from {module_stem}"
+
+
+# ─── Idempotence / --check ─────────────────────────────────────────────────────
+class TestIdempotence:
+    def test_check_flag_passes_when_current(self):
+        """`--check` should exit 0 immediately after generation."""
+        result = subprocess.run(
+            [sys.executable, str(GENERATOR), "--check"],
+            capture_output=True, text=True, cwd=REPO_ROOT, timeout=30
+        )
+        assert result.returncode == 0, (
+            f"--check failed\nSTDOUT: {{result.stdout}}\nSTDERR: {{result.stderr[:200]}}"
+        )
+
+    def test_check_fails_when_api_md_stale(self):
+        """If docs/API.md is manually altered, --check should detect staleness."""
+        # Generate fresh baseline first
+        subprocess.run([sys.executable, str(GENERATOR)], capture_output=True, cwd=REPO_ROOT, timeout=30)
+
+        # Corrupt API.md slightly (append a line at the end)
+        original = API_MD.read_text(encoding="utf-8")
+        corrupted = original + "\n<!-- corrupted -->\n"
+        API_MD.write_text(corrupted, encoding="utf-8")
+
+        # --check should now fail
+        result = subprocess.run(
+            [sys.executable, str(GENERATOR), "--check"],
+            capture_output=True, text=True, cwd=REPO_ROOT, timeout=30
+        )
+        assert result.returncode != 0, "--check should detect stale API.md"
+        assert "out-of-date" in result.stderr.lower() or "out-of-date" in result.stdout.lower()
+
+        # Restore clean state
+        subprocess.run([sys.executable, str(GENERATOR)], capture_output=True, cwd=REPO_ROOT, timeout=30)
+        assert API_MD.read_text(encoding="utf-8") == original
+
+# ─── JSON output ────────────────────────────────────────────────────────────────
+class TestJSONOutput:
+    def test_json_flag_emits_valid_json(self):
+        result = subprocess.run(
+            [sys.executable, str(GENERATOR), "--json"],
+            capture_output=True, text=True, cwd=REPO_ROOT, timeout=30
+        )
+        assert result.returncode == 0
+        import json
+        payload = json.loads(result.stdout)
+        assert "modules" in payload
+        assert len(payload["modules"]) >= 30
+
+    def test_json_has_expected_fields(self):
+        result = subprocess.run(
+            [sys.executable, str(GENERATOR), "--json"],
+            capture_output=True, text=True, cwd=REPO_ROOT, timeout=30
+        )
+        import json
+        payload = json.loads(result.stdout)
+        mod = payload["modules"][0]
+        for key in ("path", "docstring", "functions"):
+            assert key in mod, f"Missing key {{key}} in module payload"
+
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-v"])