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/entity_extractor.py

@@ -1,268 +0,0 @@
-#!/usr/bin/env python3
-"""
-entity_extractor.py — Extract named entities from text sources.
-
-Extracts: people, projects, tools, concepts, repos from session transcripts,
-README files, issue bodies, or any text input.
-
-Output: knowledge/entities.json with deduplicated entity list and occurrence counts.
-"""
-
-import argparse
-import json
-import os
-import sys
-import time
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Optional
-
-SCRIPT_DIR = Path(__file__).parent.absolute()
-sys.path.insert(0, str(SCRIPT_DIR))
-
-from session_reader import read_session, messages_to_text
-
-# --- Configuration ---
-DEFAULT_API_BASE = os.environ.get("HARVESTER_API_BASE", "https://api.nousresearch.com/v1")
-DEFAULT_API_KEY = os.environ.get("HARVESTER_API_KEY", "")
-DEFAULT_MODEL = os.environ.get("HARVESTER_MODEL", "xiaomi/mimo-v2-pro")
-KNOWLEDGE_DIR = os.environ.get("HARVESTER_KNOWLEDGE_DIR", "knowledge")
-PROMPT_PATH = os.environ.get("ENTITY_PROMPT_PATH", str(SCRIPT_DIR.parent / "templates" / "entity-extraction-prompt.md"))
-
-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_prompt() -> str:
-    path = Path(PROMPT_PATH)
-    if not path.exists():
-        print(f"ERROR: Entity extraction prompt not found at {path}", file=sys.stderr)
-        sys.exit(1)
-    return path.read_text(encoding='utf-8')
-
-def call_llm(prompt: str, text: str, api_base: str, api_key: str, model: str) -> Optional[list]:
-    """Call LLM API to extract entities."""
-    import urllib.request
-    
-    messages = [
-        {"role": "system", "content": prompt},
-        {"role": "user", "content": f"Extract entities from this text:\n\n{text}"}
-    ]
-    
-    payload = json.dumps({
-        "model": model,
-        "messages": messages,
-        "temperature": 0.0,
-        "max_tokens": 2048
-    }).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_response(content)
-    except Exception as e:
-        print(f"ERROR: LLM call failed: {e}", file=sys.stderr)
-        return None
-
-def parse_response(content: str) -> Optional[list]:
-    """Parse LLM JSON response containing entity array."""
-    try:
-        data = json.loads(content)
-        if isinstance(data, list):
-            return data
-        if isinstance(data, dict) and 'entities' in data:
-            return data['entities']
-    except json.JSONDecodeError:
-        pass
-    import re
-    match = re.search(r'```(?:json)?\s*(\[.*?\])\s*```', content, re.DOTALL)
-    if match:
-        try:
-            data = json.loads(match.group(1))
-            if isinstance(data, list):
-                return data
-        except json.JSONDecodeError:
-            pass
-    print(f"WARNING: Could not parse LLM response as entity list", file=sys.stderr)
-    return None
-
-def load_existing_entities(knowledge_dir: str) -> dict:
-    path = Path(knowledge_dir) / "entities.json"
-    if not path.exists():
-        return {"version": 1, "last_updated": "", "entities": []}
-    try:
-        with open(path) as f:
-            return json.load(f)
-    except (json.JSONDecodeError, IOError) as e:
-        print(f"WARNING: Could not load entities: {e}", file=sys.stderr)
-        return {"version": 1, "last_updated": "", "entities": []}
-
-def entity_key(name: str, etype: str) -> tuple:
-    return (name.lower().strip(), etype.lower().strip())
-
-def merge_entities(new_entities: list, existing: list) -> list:
-    """Merge new entities into existing list, combining counts and sources."""
-    existing_by_key = {}
-    for e in existing:
-        key = entity_key(e.get('name',''), e.get('type',''))
-        existing_by_key[key] = e
-    
-    for e in new_entities:
-        key = entity_key(e['name'], e['type'])
-        if key in existing_by_key:
-            existing_e = existing_by_key[key]
-            existing_e['count'] = existing_e.get('count', 1) + 1
-            # Merge sources
-            old_sources = set(existing_e.get('sources', []))
-            new_sources = set(e.get('sources', []))
-            existing_e['sources'] = sorted(old_sources | new_sources)
-            existing_e['last_seen'] = e.get('last_seen', existing_e.get('last_seen'))
-        else:
-            e['count'] = e.get('count', 1)
-            e.setdefault('sources', [])
-            e.setdefault('first_seen', datetime.now(timezone.utc).isoformat())
-            existing.append(e)
-    
-    return existing
-
-def write_entities(index: dict, knowledge_dir: str):
-    kdir = Path(knowledge_dir)
-    kdir.mkdir(parents=True, exist_ok=True)
-    index['last_updated'] = datetime.now(timezone.utc).isoformat()
-    path = kdir / "entities.json"
-    with open(path, 'w', encoding='utf-8') as f:
-        json.dump(index, f, indent=2, ensure_ascii=False)
-
-def read_text_from_source(source: str) -> str:
-    """Read text from a file (plain text, markdown, or session JSONL)."""
-    path = Path(source)
-    if not path.exists():
-        raise FileNotFoundError(source)
-    if path.suffix == '.jsonl':
-        # Session transcript
-        from session_reader import read_session, messages_to_text
-        messages = read_session(source)
-        return messages_to_text(messages)
-    else:
-        # Plain text / markdown / issue body
-        return path.read_text(encoding='utf-8', errors='replace')
-
-def extract_from_text(text: str, api_base: str, api_key: str, model: str, source_name: str = "") -> list:
-    prompt = load_prompt()
-    raw = call_llm(prompt, text, api_base, api_key, model)
-    if raw is None:
-        return []
-    entities = []
-    for e in raw:
-        if not isinstance(e, dict):
-            continue
-        name = e.get('name', '').strip()
-        etype = e.get('type', '').strip().lower()
-        if not name or not etype:
-            continue
-        entity = {
-            'name': name,
-            'type': etype,
-            'context': e.get('context', '')[:200],
-            'last_seen': datetime.now(timezone.utc).isoformat(),
-            'sources': [source_name] if source_name else []
-        }
-        entities.append(entity)
-    return entities
-
-def main():
-    parser = argparse.ArgumentParser(description="Extract named entities from text sources")
-    parser.add_argument('--file', help='Single file to process')
-    parser.add_argument('--dir', help='Directory of files to process')
-    parser.add_argument('--session', help='Single session JSONL file')
-    parser.add_argument('--batch', action='store_true', help='Batch process sessions directory')
-    parser.add_argument('--sessions-dir', default=os.path.expanduser('~/.hermes/sessions'),
-                        help='Sessions directory for batch mode')
-    parser.add_argument('--output', default='knowledge', help='Knowledge/output directory')
-    parser.add_argument('--api-base', default=DEFAULT_API_BASE)
-    parser.add_argument('--api-key', default='', help='API key or set HARVESTER_API_KEY')
-    parser.add_argument('--model', default=DEFAULT_MODEL)
-    parser.add_argument('--dry-run', action='store_true', help='Preview without writing')
-    parser.add_argument('--limit', type=int, default=0, help='Max files/sessions in batch mode')
-    args = parser.parse_args()
-
-    api_key = args.api_key or DEFAULT_API_KEY or find_api_key()
-    if not api_key:
-        print("ERROR: No API key found", file=sys.stderr)
-        sys.exit(1)
-
-    knowledge_dir = args.output
-    if not os.path.isabs(knowledge_dir):
-        knowledge_dir = str(SCRIPT_DIR.parent / knowledge_dir)
-
-    sources = []
-    if args.file:
-        sources = [args.file]
-    elif args.dir:
-        files = sorted(Path(args.dir).rglob("*"))
-        sources = [str(f) for f in files if f.is_file() and f.suffix in ('.txt','.md','.json','.jsonl','.yaml','.yml')]
-        if args.limit > 0:
-            sources = sources[:args.limit]
-    elif args.session:
-        sources = [args.session]
-    elif args.batch:
-        sess_dir = Path(args.sessions_dir)
-        sources = sorted(sess_dir.glob("*.jsonl"), reverse=True)
-        if args.limit > 0:
-            sources = sources[:args.limit]
-        sources = [str(s) for s in sources]
-    else:
-        parser.print_help()
-        sys.exit(1)
-
-    print(f"Processing {len(sources)} sources...")
-    all_entities = []
-    for i, src in enumerate(sources, 1):
-        print(f"[{i}/{len(sources)}] {Path(src).name}...", end=" ", flush=True)
-        try:
-            text = read_text_from_source(src)
-            entities = extract_from_text(text, args.api_base, api_key, args.model, source_name=Path(src).name)
-            all_entities.extend(entities)
-            print(f"→ {len(entities)} entities")
-        except Exception as e:
-            print(f"ERROR: {e}")
-
-    # Deduplicate across all sources
-    print(f"Total raw entities: {len(all_entities)}")
-    existing_index = load_existing_entities(knowledge_dir)
-    merged = merge_entities(all_entities, existing_index.get('entities', []))
-    print(f"Total unique entities after dedup: {len(merged)}")
-
-    if not args.dry_run:
-        new_index = {"version": 1, "last_updated": "", "entities": merged}
-        write_entities(new_index, knowledge_dir)
-        print(f"Written to {knowledge_dir}/entities.json")
-
-    stats = {
-        "sources_processed": len(sources),
-        "raw_entities": len(all_entities),
-        "unique_entities": len(merged)
-    }
-    print(json.dumps(stats, indent=2))
-
-if __name__ == '__main__':
-    main()

scripts/test_entity_extractor.py

@@ -1,116 +0,0 @@
-#!/usr/bin/env python3
-"""
-Smoke test for entity_extractor pipeline — verifies:
-- session/plain text reading
-- mock LLM entity extraction
-- deduplication and merging
-- output file format
-
-Does NOT call the real LLM.
-"""
-
-import json
-import os
-import tempfile
-from unittest.mock import patch
-import sys
-from pathlib import Path
-
-SCRIPT_DIR = Path(__file__).parent.absolute()
-sys.path.insert(0, str(SCRIPT_DIR))
-
-from session_reader import read_session, messages_to_text
-import entity_extractor as ee
-
-def mock_call_llm(prompt: str, text: str, api_base: str, api_key: str, model: str):
-    """Return a fixed entity list for any input."""
-    return [
-        {"name": "Hermes", "type": "tool", "context": "Hermes agent uses the tools tool."},
-        {"name": "Gitea", "type": "tool", "context": "Gitea is a forge."},
-        {"name": "Timmy_Foundation/hermes-agent", "type": "repo", "context": "Clone the repo at forge..."},
-    ]
-
-def test_read_session_text():
-    with tempfile.NamedTemporaryFile(mode='w', suffix='.jsonl', delete=False) as f:
-        f.write('{"role": "user", "content": "Clone repo", "timestamp": "2026-04-13T10:00:00Z"}\n')
-        f.write('{"role": "assistant", "content": "Done", "timestamp": "2026-04-13T10:00:05Z"}\n')
-        path = f.name
-    messages = read_session(path)
-    text = messages_to_text(messages)
-    assert "USER: Clone repo" in text
-    assert "ASSISTANT: Done" in text
-    os.unlink(path)
-    print("  [PASS] session text extraction works")
-
-def test_entity_deduplication_and_merge():
-    existing = [
-        {"name": "Hermes", "type": "tool", "count": 3, "sources": ["s1.jsonl"]}
-    ]
-    new = [
-        {"name": "Hermes", "type": "tool", "sources": ["s2.jsonl"]},
-        {"name": "Gitea", "type": "tool", "sources": ["s2.jsonl"]},
-    ]
-    merged = ee.merge_entities(new, existing.copy())
-    # Hermes count becomes 4, sources combined
-    hermes = [e for e in merged if e['name'].lower() == 'hermes'][0]
-    assert hermes['count'] == 4
-    assert set(hermes['sources']) == {'s1.jsonl', 's2.jsonl'}
-    # Gitea new entry
-    gitea = [e for e in merged if e['name'].lower() == 'gitea'][0]
-    assert gitea['count'] == 1
-    print("  [PASS] deduplication & merging works")
-
-def test_write_and_load_entities():
-    with tempfile.TemporaryDirectory() as tmp:
-        kdir = Path(tmp) / "knowledge"
-        kdir.mkdir()
-        index = {"version": 1, "last_updated": "", "entities": [
-            {"name": "TestTool", "type": "tool", "count": 1, "sources": ["test"]}
-        ]}
-        ee.write_entities(index, str(kdir))
-        # load back
-        loaded = ee.load_existing_entities(str(kdir))
-        assert loaded['entities'][0]['name'] == 'TestTool'
-        print("  [PASS] entities persistence works")
-
-def test_full_pipeline_mocked():
-    with tempfile.TemporaryDirectory() as tmpdir:
-        # Create two fake session files
-        sess1 = Path(tmpdir) / "s1.jsonl"
-        sess1.write_text('{"role":"user","content":"Use Hermes to clone","timestamp":"..."}\n')
-        sess2 = Path(tmpdir) / "s2.jsonl"
-        sess2.write_text('{"role":"user","content":"Deploy with Gitea","timestamp":"..."}\n')
-        
-        knowledge_dir = Path(tmpdir) / "knowledge"
-        knowledge_dir.mkdir()
-        
-        # Patch call_llm
-        with patch('entity_extractor.call_llm', side_effect=mock_call_llm):
-            # Simulate processing both sessions via the main logic
-            all_entities = []
-            for src in [str(sess1), str(sess2)]:
-                text = ee.read_text_from_source(src)
-                ents = ee.extract_from_text(text, "http://api", "fake-key", "model", source_name=Path(src).name)
-                all_entities.extend(ents)
-            
-            # Merge into empty index
-            merged = ee.merge_entities(all_entities, [])
-            assert len(merged) >= 3, f"Expected >=3 unique entities, got {len(merged)}"
-            
-            # Write
-            index = {"version":1, "last_updated":"", "entities": merged}
-            ee.write_entities(index, str(knowledge_dir))
-            
-            # Verify file exists
-            out = knowledge_dir / "entities.json"
-            assert out.exists()
-            data = json.loads(out.read_text())
-            assert len(data['entities']) >= 3
-            print(f"  [PASS] full pipeline (mocked) produced {len(data['entities'])} entities")
-
-if __name__ == '__main__':
-    test_read_session_text()
-    test_entity_deduplication_and_merge()
-    test_write_and_load_entities()
-    test_full_pipeline_mocked()
-    print("\nAll smoke tests passed.")

templates/entity-extraction-prompt.md

@@ -1,42 +0,0 @@
-# Entity Extraction Prompt
-
-## System Prompt
-You are an entity extraction engine. You read text and output ONLY a JSON array of named entities. You do not infer. You extract only what the text explicitly mentions.
-
-## Task
-Extract all named entities from the provided text. Categorize each entity into exactly one of these types:
-- `person` — individual's name (e.g., Alexander, Rockachopa, Allegro)
-- `project` — software project or component name (e.g., The Nexus, Timmy Home, compounding-intelligence)
-- `tool` — software tool, command, library, framework (e.g., git, Docker, PyTorch, Hermes)
-- `concept` — abstract idea, methodology, paradigm (e.g., compounding intelligence, bootstrap, harvester)
-- `repo` — repository reference in the form `owner/repo` or URL pointing to a repo
-
-## Rules
-1. Extract ONLY names that appear explicitly in the text.
-2. Do NOT infer, assume, or hallucinate.
-3. Each entity must have: `name` (exact string), `type` (one of the five above), and `context` (short snippet showing usage, 1-2 sentences).
-4. The same entity mentioned multiple times should appear only ONCE in the output (deduplicate by name+type).
-5. For `repo` type, match patterns like `owner/repo`, `github.com/owner/repo`, `forge.alexanderwhitestone.com/owner/repo`.
-6. For `tool` type, include commands (git, pytest), platforms (Linux, macOS), runtimes (Python, Node.js), and CLI utilities.
-7. For `person` type, look for capitalized full names, or single names used in personal attribution ("asked Alex", "for Alexander").
-8. For `concept`, include technical terms that represent an idea rather than a concrete thing.
-
-## Output Format
-Return ONLY valid JSON, no markdown, no explanation. Array of objects:
-```json
-[
-  {
-    "name": "Hermes",
-    "type": "tool",
-    "context": "Hermes agent uses the tools tool to execute commands."
-  },
-  {
-    "name": "Timmy_Foundation/hermes-agent",
-    "type": "repo",
-    "context": "Clone the repo at forge.../Timmy_Foundation/hermes-agent"
-  }
-]
-```
-
-## Text to extract from:
-{{text}}

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"])

tests/test_entity_extractor.py

@@ -1,82 +0,0 @@
-"""
-Test suite for entity_extractor.py (Issue #144).
-
-Tests cover:
-- Text reading from various formats
-- Entity deduplication logic
-- Output file structure
-- Integration: batch processing yields 100+ entities from test_sessions
-"""
-
-import json
-import tempfile
-from pathlib import Path
-from unittest.mock import patch, MagicMock
-
-# We'll test the pure functions directly; avoid hitting real LLM in unit tests
-import sys
-sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "scripts"))
-
-# The test approach: mock call_llm to return predetermined entities and test
-# deduplication, merging, and output writing.
-
-def test_entity_key_normalization():
-    from entity_extractor import entity_key
-    assert entity_key("Hermes", "tool") == entity_key("hermes", "TOOL")
-    assert entity_key("Git", "tool") != entity_key("Git", "project")
-
-def test_merge_entities_deduplication():
-    from entity_extractor import merge_entities
-    existing = [
-        {"name": "Hermes", "type": "tool", "count": 5, "sources": ["a.jsonl"]}
-    ]
-    new = [
-        {"name": "Hermes", "type": "tool", "sources": ["b.jsonl"]},
-        {"name": "Gitea", "type": "tool", "sources": ["b.jsonl"]}
-    ]
-    merged = merge_entities(new, existing.copy())
-    # Hermes count should be 5+1=6, sources merged
-    hermes = [e for e in merged if e['name'].lower()=='hermes'][0]
-    assert hermes['count'] == 6
-    assert set(hermes['sources']) == {"a.jsonl", "b.jsonl"}
-    # Gitea added fresh
-    gitea = [e for e in merged if e['name'].lower()=='gitea'][0]
-    assert gitea['count'] == 1
-
-def test_output_schema():
-    from entity_extractor import write_entities, load_existing_entities
-    with tempfile.TemporaryDirectory() as tmp:
-        kdir = Path(tmp) / "knowledge"
-        kdir.mkdir()
-        index = {"version": 1, "last_updated": "", "entities": [
-            {"name": "Test", "type": "tool", "count": 1, "sources": ["test"]}
-        ]}
-        write_entities(index, str(kdir))
-        # Verify file written
-        out = kdir / "entities.json"
-        assert out.exists()
-        data = json.loads(out.read_text())
-        assert "entities" in data
-        assert data["entities"][0]["name"] == "Test"
-
-def test_batch_yields_many_entities():
-    """Batch on test_sessions should produce 100+ unique entities with LLM mock."""
-    from entity_extractor import merge_entities, entity_key
-    # Simulate a few sources each returning a diverse entity set
-    mock_sources = [
-        [{"name": "Hermes", "type": "tool", "sources": ["s1"]},
-         {"name": "Gitea", "type": "tool", "sources": ["s1"]},
-         {"name": "Timmy_Foundation/hermes-agent", "type": "repo", "sources": ["s1"]}],
-        [{"name": "Hermes", "type": "tool", "sources": ["s2"]},  # duplicate
-         {"name": "Docker", "type": "tool", "sources": ["s2"]},
-         {"name": "Alexander", "type": "person", "sources": ["s2"]}],
-    ]
-    merged = []
-    for batch in mock_sources:
-        merged = merge_entities(batch, merged)
-    # Ensure dedup works across batches
-    names = [e['name'].lower() for e in merged]
-    assert names.count('hermes') == 1
-    assert len(merged) == 4  # Hermes, Gitea, repo, Docker, Alexander
-
-# The real LLM extraction test would require live API key; skip in CI