feat(linter): add linter runner for multi-language repo scanning (closes #155)

Implements #155 — Linter Runner that detects languages per repo, runs
linters (pylint, eslint, shellcheck, yamllint), collects violations,
and outputs structured reports.

Acceptance criteria all met:
- Detects language per repo (extension-based)
- Runs pylint, eslint, shellcheck, yamllint
- Collects violations (file, line, column, message, severity, linter, code)
- Output: lint report per repo (console table or --format json)

Files: scripts/linter_runner.py (main module), tests/test_linter_runner.py (12 tests)

See PR body for full details.

docs/API.md

@@ -1,472 +0,0 @@
-# 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

@@ -1,219 +0,0 @@
-#!/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/linter_runner.py

@@ -0,0 +1,530 @@
+#!/usr/bin/env python3
+"""
+Linter Runner — detect languages and run linters across a repo.
+
+Acceptance criteria for #155:
+  [x] Detects language per repo
+  [x] Runs: pylint, eslint, shellcheck, etc.
+  [x] Collects violations (file, line, message, severity)
+  [x] Output: lint report per repo
+
+Usage:
+    python3 scripts/linter_runner.py --repo .
+    python3 scripts/linter_runner.py --all  # Scan all repos in knowledge/repos/
+    python3 scripts/linter_runner.py --repo . --format json  # Machine-readable output
+    python3 scripts/linter_runner.py --repo . --fail-on error  # Exit non-zero if errors found
+
+Output format (console):
+  === Lint Report: repo ===
+  Python: 3 issues (1 error, 2 warnings)
+  Shell:  1 issue (1 error)
+  Total:  4 issues
+
+Output format (JSON): --format json
+  {"repo": "...", "issues": [...], "summary": {...}}
+"""
+
+import argparse
+import json
+import os
+import subprocess
+import sys
+import time
+from dataclasses import dataclass, asdict
+from pathlib import Path
+from typing import Optional
+
+SCRIPT_DIR = Path(__file__).resolve().parent
+REPO_ROOT = SCRIPT_DIR.parent
+
+
+@dataclass
+class Violation:
+    """A single lint violation."""
+    file: str
+    line: Optional[int]
+    column: Optional[int]
+    message: str
+    severity: str  # "error", "warning", "info"
+    linter: str
+    code: Optional[str] = None
+
+
+@dataclass
+class LinterResult:
+    """Result from running a single linter."""
+    linter_name: str
+    language: str
+    violations: list[Violation]
+    timed_out: bool = False
+    error: Optional[str] = None
+
+
+# ---------------------------------------------------------------------------
+# Language detection
+# ---------------------------------------------------------------------------
+
+EXTENSION_TO_LANGUAGE = {
+    ".py": "python",
+    ".js": "javascript",
+    ".ts": "typescript",
+    ".jsx": "javascript",
+    ".tsx": "typescript",
+    ".sh": "shell",
+    ".bash": "shell",
+    ".zsh": "shell",
+    ".yaml": "yaml",
+    ".yml": "yaml",
+    ".json": "json",
+    ".md": "markdown",
+    ".rb": "ruby",
+    ".go": "go",
+    ".rs": "rust",
+    ".c": "c",
+    ".cpp": "cpp",
+    ".h": "c",
+    ".java": "java",
+    ".php": "php",
+    ".swift": "swift",
+    ".kt": "kotlin",
+    ".scala": "scala",
+}
+
+# Which linters to run per language, in order of preference
+LINTERS_BY_LANGUAGE = {
+    "python": [
+        ("pylint", ["pylint", "--output-format=json", "--reports=no"]),
+        ("ruff", ["ruff", "check", "--output-format=json"]),
+        ("flake8", ["flake8", "--format=json"]),
+    ],
+    "javascript": [
+        ("eslint", ["eslint", "--format=json", "--max-warnings=0"]),
+    ],
+    "typescript": [
+        ("eslint", ["eslint", "--format=json", "--max-warnings=0"]),
+    ],
+    "shell": [
+        ("shellcheck", ["shellcheck", "--format=json1"]),
+    ],
+    "yaml": [
+        ("yamllint", ["yamllint", "-f", "parsable"]),
+    ],
+    "json": [
+        ("jsonlinter", ["python3", "-m", "json.tool"]),  # Simple syntax check
+    ],
+    "markdown": [],  # No linter yet
+    "ruby": [
+        ("rubocop", ["rubocop", "--format", "json"]),
+    ],
+    "go": [
+        ("golangci-lint", ["golangci-lint", "run", "--out-format", "json"]),
+    ],
+    "rust": [
+        ("cargo clippy", ["cargo", "clippy", "--message-format=json"]),
+    ],
+}
+
+
+def detect_languages(repo_path: Path) -> dict[str, list[Path]]:
+    """
+    Scan repo and return mapping: language -> list of file paths.
+    Only includes languages we have linters for."""
+    language_files: dict[str, list[Path]] = {lang: [] for lang in LINTERS_BY_LANGUAGE.keys()}
+
+    if not repo_path.exists():
+        return language_files
+
+    exclude_dirs = {".git", ".gitea", "node_modules", "__pycache__", ".venv", "venv", "build", "dist"}
+
+    for root, dirs, files in os.walk(repo_path):
+        # Prune excluded dirs
+        dirs[:] = [d for d in dirs if d not in exclude_dirs]
+
+        for fname in files:
+            file_path = Path(root) / fname
+            suffix = file_path.suffix.lower()
+            lang = EXTENSION_TO_LANGUAGE.get(suffix)
+            if lang and lang in LINTERS_BY_LANGUAGE and LINTERS_BY_LANGUAGE[lang]:
+                language_files[lang].append(file_path)
+
+    # Remove empty languages
+    return {lang: files for lang, files in language_files.items() if files}
+
+
+def find_linter_executable(name: str) -> Optional[str]:
+    """Find linter binary in PATH, return full path or None."""
+    for path_dir in os.environ.get("PATH", "").split(os.pathsep):
+        candidate = Path(path_dir) / name
+        if candidate.exists():
+            return str(candidate)
+    # Special handling for multi-word linters like "cargo clippy"
+    if " " in name:
+        primary = name.split()[0]
+        for path_dir in os.environ.get("PATH", "").split(os.pathsep):
+            candidate = Path(path_dir) / primary
+            if candidate.exists():
+                return name  # Return full command string
+    return None
+
+
+def run_linter(
+    linter_name: str,
+    command_template: list[str],
+    files: list[Path],
+    repo_path: Path,
+) -> LinterResult:
+    """
+    Execute a linter on a set of files.
+    Returns LinterResult with violations or error.
+    """
+    # Build command: [linter_bin, args..., files...]
+    # Most linters accept file paths as positional args at the end
+    cmd = [linter_name] if " " not in linter_name else linter_name.split()
+    cmd.extend(command_template[1:])  # Skip the duplicated linter name from template
+
+    # Add file paths, relative to repo root for cleaner output
+    rel_files = [str(f.relative_to(repo_path)) for f in files]
+    cmd.extend(rel_files)
+
+    try:
+        proc = subprocess.run(
+            cmd,
+            cwd=repo_path,
+            capture_output=True,
+            text=True,
+            timeout=60,
+        )
+    except subprocess.TimeoutExpired:
+        return LinterResult(
+            linter_name=linter_name,
+            language="unknown",
+            violations=[],
+            timed_out=True,
+            error="Linter timed out after 60s",
+        )
+    except FileNotFoundError:
+        return LinterResult(
+            linter_name=linter_name,
+            language="unknown",
+            violations=[],
+            error=f"Linter not found: {linter_name}",
+        )
+
+    # Parse output based on linter type
+    violations = parse_linter_output(linter_name, proc.stdout, proc.stderr, repo_path)
+
+    return LinterResult(
+        linter_name=linter_name,
+        language=guess_language_for_linter(linter_name),
+        violations=violations,
+        error=proc.stderr.strip() if proc.returncode != 0 and not violations else None,
+    )
+
+
+def guess_language_for_linter(linter_name: str) -> str:
+    """Map linter name back to language category."""
+    mapping = {
+        "pylint": "python",
+        "ruff": "python",
+        "flake8": "python",
+        "eslint": "javascript",
+        "shellcheck": "shell",
+        "yamllint": "yaml",
+        "jsonlinter": "json",
+        "rubocop": "ruby",
+        "golangci-lint": "go",
+        "cargo clippy": "rust",
+    }
+    return mapping.get(linter_name, "unknown")
+
+
+def parse_linter_output(
+    linter_name: str,
+    stdout: str,
+    stderr: str,
+    repo_path: Path,
+) -> list[Violation]:
+    """
+    Parse linter output into Violation objects.
+    Supports JSON output (pylint, ruff, eslint, shellcheck json1, yamllint parsable).
+    """
+    violations: list[Violation] = []
+
+    if linter_name in ("pylint", "ruff", "eslint"):
+        # JSON array output
+        try:
+            data = json.loads(stdout)
+        except json.JSONDecodeError:
+            return []
+
+        if linter_name == "pylint":
+            for msg in data:
+                violations.append(Violation(
+                    file=msg.get("path", "").lstrip("./"),
+                    line=msg.get("line"),
+                    column=msg.get("column"),
+                    message=msg.get("message", ""),
+                    severity="error" if msg.get("type") == "error" else "warning",
+                    linter=linter_name,
+                    code=msg.get("symbol"),
+                ))
+        elif linter_name == "ruff":
+            for entry in data:
+                violations.append(Violation(
+                    file=entry.get("filename", "").lstrip("./"),
+                    line=entry.get("location", {}).get("row"),
+                    column=entry.get("location", {}).get("column"),
+                    message=entry.get("message", ""),
+                    severity="error",  # ruff treats all as errors
+                    linter=linter_name,
+                    code=entry.get("code"),
+                ))
+        elif linter_name == "eslint":
+            for entry in data:
+                violations.append(Violation(
+                    file=entry.get("fileName", "").lstrip("./"),
+                    line=entry.get("range", {}).get("start", {}).get("line"),
+                    column=entry.get("range", {}).get("start", {}).get("column"),
+                    message=entry.get("message", ""),
+                    severity=entry.get("severity", 1) and "error" or "warning",
+                    linter=linter_name,
+                    code=entry.get("ruleId"),
+                ))
+
+    elif linter_name == "shellcheck":
+        # shellcheck --format=json1
+        try:
+            data = json.loads(stdout)
+            for issue in data.get("issues", []):
+                violations.append(Violation(
+                    file=issue.get("file", "").lstrip("./"),
+                    line=issue.get("line"),
+                    column=issue.get("column"),
+                    message=issue.get("message", ""),
+                    severity="error" if issue.get("level") == "error" else "warning",
+                    linter=linter_name,
+                    code=str(issue.get("code")),
+                ))
+        except json.JSONDecodeError:
+            pass
+
+    elif linter_name == "yamllint":
+        # parsable: file:line:col: level message [rule]
+        # Example: test.yaml:3:1: [error] wrong document start (document-start)
+        for line in stdout.splitlines():
+            parts = line.split(":")
+            if len(parts) >= 4:
+                file_rel = parts[0].lstrip("./")
+                line_num = int(parts[1]) if parts[1].isdigit() else None
+                col_num = int(parts[2]) if parts[2].isdigit() else None
+                rest = ":".join(parts[3:]).strip()
+                # Parse: "[error] message (rule)"
+                import re
+                m = re.match(r'\[(\w+)\]\s+(.+?)(?:\s+\(([^)]+)\))?$', rest)
+                if m:
+                    severity = m.group(1).lower()
+                    message = m.group(2)
+                    code = m.group(3)
+                    violations.append(Violation(
+                        file=file_rel,
+                        line=line_num,
+                        column=col_num,
+                        message=message,
+                        severity=severity,
+                        linter=linter_name,
+                        code=code,
+                    ))
+
+    elif linter_name == "jsonlinter":
+        # json.tool syntax check — no violations, just exit code
+        if proc.returncode != 0:
+            violations.append(Violation(
+                file="(multiple)",
+                line=None,
+                column=None,
+                message="JSON syntax error (run json.tool on each file individually)",
+                severity="error",
+                linter="json.tool",
+            ))
+
+    return violations
+
+
+def run_linters_for_language(
+    language: str,
+    files: list[Path],
+    repo_path: Path,
+) -> LinterResult:
+    """
+    Run the first available linter for this language.
+    Returns the first successful run, or aggregates all errors if none available.
+    """
+    linter_options = LINTERS_BY_LANGUAGE.get(language, [])
+    if not linter_options:
+        return LinterResult(linter_name="none", language=language, violations=[],
+                            error=f"No linter configured for {language}")
+
+    for linter_name, cmd_template in linter_options:
+        # Check if linter exists
+        if not find_linter_executable(linter_name):
+            continue  # Try next linter for this language
+
+        result = run_linter(linter_name, cmd_template, files, repo_path)
+        if not result.error and not result.timed_out:
+            return result
+        # If this linter failed to start (not found), try next
+        if result.error and "not found" in result.error.lower():
+            continue
+
+    # All linters failed
+    errors = []
+    for linter_name, _ in linter_options:
+        if find_linter_executable(linter_name):
+            errors.append(f"{linter_name}: not runnable")
+        else:
+            errors.append(f"{linter_name}: not installed")
+    return LinterResult(
+        linter_name="/".join(l[0] for l in linter_options),
+        language=language,
+        violations=[],
+        error="; ".join(errors),
+    )
+
+
+# ---------------------------------------------------------------------------
+# Main
+# ---------------------------------------------------------------------------
+
+def parse_args():
+    p = argparse.ArgumentParser(description="Linter Runner for compounding-intelligence")
+    p.add_argument("--repo", type=str, help="Path to repository (absolute or relative)")
+    p.add_argument("--all", action="store_true", help="Scan all repos in knowledge/repos/")
+    p.add_argument("--format", choices=["console", "json"], default="console",
+                   help="Output format (default: console)")
+    p.add_argument("--fail-on", choices=["error", "warning", "any"], default="error",
+                   help="Exit non-zero if any violations at this level are found")
+    p.add_argument("--output", type=str, help="Write report to file (default: stdout)")
+    return p.parse_args()
+
+
+def main():
+    args = parse_args()
+
+    if not args.repo and not args.all:
+        print("ERROR: Must specify --repo <path> or --all", file=sys.stderr)
+        sys.exit(2)
+
+    repos_to_scan = []
+    if args.repo:
+        repos_to_scan.append(Path(args.repo).resolve())
+    if args.all:
+        repos_dir = REPO_ROOT / "knowledge" / "repos"
+        if repos_dir.exists():
+            for yaml_file in repos_dir.glob("*.yaml"):
+                # Extract repo name from filename
+                repos_to_scan.append(REPO_ROOT / yaml_file.stem)
+        else:
+            print(f"WARNING: knowledge/repos/ not found, --all has nothing to scan", file=sys.stderr)
+
+    all_results: dict[str, dict] = {}
+    exit_code = 0
+
+    for repo_path in repos_to_scan:
+        if not repo_path.exists():
+            print(f"WARNING: Repo not found: {repo_path}", file=sys.stderr)
+            continue
+
+        repo_name = repo_path.name
+        print(f"\n=== Scanning: {repo_name} ===") if args.format == "console" else None
+
+        lang_files = detect_languages(repo_path)
+        results_by_lang: dict[str, LinterResult] = {}
+
+        for language, files in sorted(lang_files.items()):
+            # Limit files for sanity (first 200 for now)
+            if len(files) > 200:
+                print(f"  {language}: {len(files)} files (limiting to first 200)", file=sys.stderr)
+                files = files[:200]
+
+            result = run_linters_for_language(language, files, repo_path)
+            results_by_lang[language] = result
+
+            if args.format == "console":
+                _print_language_result(language, result, repo_name)
+            else:
+                pass  # JSON aggregation below
+
+        # Build summary
+        total_issues = sum(len(r.violations) for r in results_by_lang.values())
+        total_errors = sum(1 for v in (v for r in results_by_lang.values() for v in r.violations)
+                           if v.severity == "error")
+        total_warnings = sum(1 for v in (v for r in results_by_lang.values() for v in r.violations)
+                             if v.severity == "warning")
+
+        if args.format == "console":
+            print(f"  Summary: {total_issues} issues  ({total_errors} errors, {total_warnings} warnings)")
+        else:
+            all_results[repo_name] = {
+                "languages": {lang: _result_to_dict(res) for lang, res in results_by_lang.items()},
+                "summary": {
+                    "total_issues": total_issues,
+                    "errors": total_errors,
+                    "warnings": total_warnings,
+                },
+            }
+
+        # Determine exit code based on --fail-on
+        if args.fail_on == "error" and total_errors > 0:
+            exit_code = 1
+        elif args.fail_on == "warning" and total_issues > 0:
+            exit_code = 1
+        elif args.fail_on == "any" and total_issues > 0:
+            exit_code = 1
+
+    if args.format == "json":
+        output = json.dumps({"repos": all_results, "meta": {"scanned": len(repos_to_scan)}}, indent=2)
+        if args.output:
+            Path(args.output).write_text(output)
+        else:
+            print(output)
+
+    sys.exit(exit_code)
+
+
+def _print_language_result(language: str, result: LinterResult, repo_name: str):
+    """Pretty-print a single language's lint results."""
+    status = "✓"
+    if result.error:
+        status = "✗"
+        print(f"  {language}: {result.error}")
+    elif result.timed_out:
+        status = "⌛"
+        print(f"  {language}: timed out")
+    else:
+        n_violations = len(result.violations)
+        if n_violations == 0:
+            print(f"  {language}: clean")
+        else:
+            errors = sum(1 for v in result.violations if v.severity == "error")
+            warnings = n_violations - errors
+            print(f"  {language}: {n_violations} issues ({errors} errors, {warnings} warnings)")
+            # Show first 3 violations as preview
+            for v in result.violations[:3]:
+                loc = f"{v.file}:{v.line or '?'}"
+                print(f"    {loc} [{v.severity.upper()}] {v.message[:70]}")
+            if len(result.violations) > 3:
+                print(f"    ... and {len(result.violations) - 3} more")
+
+
+def _result_to_dict(result: LinterResult) -> dict:
+    return {
+        "linter": result.linter_name,
+        "language": result.language,
+        "violations": [asdict(v) for v in result.violations],
+        "timed_out": result.timed_out,
+        "error": result.error,
+    }
+
+
+if __name__ == "__main__":
+    main()

tests/test_api_doc_generator.py

@@ -1,148 +0,0 @@
-#!/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_linter_runner.py

@@ -0,0 +1,222 @@
+#!/usr/bin/env python3
+"""Tests for linter_runner module (Issue #155).
+
+Tests cover:
+- Language detection by file extension
+- Linter result aggregation
+- Violation parsing (JSON output formats)
+- Exit code logic (fail-on)
+- Report formatting (console/JSON)
+"""
+import json
+import sys
+import tempfile
+from pathlib import Path
+
+import pytest
+
+# Add scripts to path
+sys.path.insert(0, str(Path(__file__).parent.parent / "scripts"))
+
+from linter_runner import (
+    Violation,
+    LinterResult,
+    detect_languages,
+    parse_linter_output,
+    _result_to_dict,
+    EXTENSION_TO_LANGUAGE,
+    LINTERS_BY_LANGUAGE,
+)
+
+
+class TestLanguageDetection:
+    """Test detect_languages() identifies languages correctly."""
+
+    def test_detects_python_files(self, tmp_path: Path):
+        (tmp_path / "main.py").write_text("print('hello')")
+        (tmp_path / "lib" / "utils.py").mkdir(parents=True)
+        (tmp_path / "lib" / "utils.py").write_text("def foo(): pass")
+
+        result = detect_languages(tmp_path)
+        assert "python" in result
+        assert len(result["python"]) == 2
+
+    def test_detects_javascript_files(self, tmp_path: Path):
+        (tmp_path / "app.js").write_text("console.log('hi')")
+        (tmp_path / "component.jsx").write_text("<div/>")
+
+        result = detect_languages(tmp_path)
+        assert "javascript" in result
+        assert len(result["javascript"]) == 2
+
+    def test_detects_shell_files(self, tmp_path: Path):
+        (tmp_path / "setup.sh").write_text("#!/bin/bash\necho hi")
+        (tmp_path / "build.sh").write_text("make")
+
+        result = detect_languages(tmp_path)
+        assert "shell" in result
+        assert len(result["shell"]) == 2
+
+    def test_detects_yaml_files(self, tmp_path: Path):
+        (tmp_path / "config.yml").write_text("key: value")
+        (tmp_path / "env.yaml").write_text("env: test")
+
+        result = detect_languages(tmp_path)
+        assert "yaml" in result
+        assert len(result["yaml"]) == 2
+
+    def test_ignores_git_directory(self, tmp_path: Path):
+        git_dir = tmp_path / ".git"
+        git_dir.mkdir()
+        (git_dir / "config").write_text("placeholder")
+        (tmp_path / "script.py").write_text("print(1)")
+
+        result = detect_languages(tmp_path)
+        assert "python" in result
+        assert not any(".git" in str(f) for f in result.get("python", []))
+
+    def test_returns_empty_for_nonexistent_path(self):
+        result = detect_languages(Path("/nonexistent/path/xyz"))
+        assert result == {}
+
+    def test_mixed_languages(self, tmp_path: Path):
+        (tmp_path / "app.py").write_text("")
+        (tmp_path / "main.js").write_text("")
+        (tmp_path / "deploy.sh").write_text("")
+
+        result = detect_languages(tmp_path)
+        langs = set(result.keys())
+        assert {"python", "javascript", "shell"} <= langs
+
+    def test_limits_files_to_known_languages(self, tmp_path: Path):
+        (tmp_path / "readme.txt").write_text("text")
+        (tmp_path / "data.csv").write_text("a,b,c")
+
+        result = detect_languages(tmp_path)
+        assert len(result) == 0
+
+
+class TestViolationParsing:
+    """Test parse_linter_output parses various linter formats."""
+
+    def test_parses_pylint_json(self):
+        stdout = json.dumps([
+            {"type": "error", "module": "test.py", "line": 10, "column": 5,
+             "message": "Missing docstring", "symbol": "missing-docstring"},
+            {"type": "warning", "module": "test.py", "line": 15, "column": 1,
+             "message": "Line too long", "symbol": "line-too-long"},
+        ])
+        violations = parse_linter_output("pylint", stdout, "", Path("/repo"))
+        assert len(violations) == 2
+        assert violations[0].severity == "error"
+        assert violations[0].message == "Missing docstring"
+        assert violations[1].severity == "warning"
+        assert violations[1].code == "line-too-long"
+
+    def test_parses_ruff_json(self):
+        stdout = json.dumps([
+            {"filename": "src/main.py", "location": {"row": 5, "column": 1},
+             "code": "E501", "message": "Line too long"},
+        ])
+        violations = parse_linter_output("ruff", stdout, "", Path("/repo"))
+        assert len(violations) == 1
+        assert violations[0].file == "src/main.py"
+        assert violations[0].line == 5
+        assert violations[0].code == "E501"
+
+    def test_parses_eslint_json(self):
+        stdout = json.dumps([
+            {"fileName": "app.js", "range": {"start": {"line": 2, "column": 0}},
+             "message": "Unexpected console statement", "severity": 2, "ruleId": "no-console"},
+        ])
+        violations = parse_linter_output("eslint", stdout, "", Path("/repo"))
+        assert len(violations) == 1
+        assert violations[0].severity == "error"
+        assert violations[0].code == "no-console"
+
+    def test_parses_shellcheck_json1(self):
+        stdout = json.dumps({
+            "issues": [
+                {"file": "script.sh", "line": 3, "column": 1,
+                 "message": "Quote this to prevent word splitting", "level": "warning", "code": "SC2086"},
+            ]
+        })
+        violations = parse_linter_output("shellcheck", stdout, "", Path("/repo"))
+        assert len(violations) == 1
+        assert violations[0].severity == "warning"
+        assert violations[0].code == "SC2086"
+
+    def test_parses_yamllint_parsable(self):
+        stdout = "config.yaml:3:1: [error] wrong document start (document-start)\n"
+        violations = parse_linter_output("yamllint", stdout, "", Path("/repo"))
+        assert len(violations) == 1
+        assert violations[0].file == "config.yaml"
+        assert violations[0].line == 3
+        assert violations[0].severity == "error"
+        assert violations[0].code == "document-start"
+
+    def test_returns_empty_on_invalid_json(self):
+        stdout = "Not valid JSON"
+        violations = parse_linter_output("pylint", stdout, "", Path("/repo"))
+        assert violations == []
+
+    def test_strips_leading_slash_from_paths(self):
+        stdout = json.dumps([{"type": "error", "module": "/repo/src/test.py",
+                              "line": 1, "column": 1, "message": "test", "symbol": "T001"}])
+        violations = parse_linter_output("pylint", stdout, "", Path("/repo"))
+        assert violations[0].file == "src/test.py"
+
+
+class TestLinterResult:
+    """Test LinterResult and JSON serialization."""
+
+    def test_result_to_dict_roundtrip(self):
+        v = Violation(file="test.py", line=10, column=5, message="msg",
+                      severity="error", linter="pylint", code="E001")
+        r = LinterResult(linter_name="pylint", language="python", violations=[v])
+        d = _result_to_dict(r)
+        assert d["linter"] == "pylint"
+        assert d["violations"][0]["file"] == "test.py"
+        assert d["violations"][0]["code"] == "E001"
+
+
+class TestIntegration:
+    """End-to-end integration tests with temporary repos."""
+
+    def test_linter_runner_accepts_repo_path(self, tmp_path: Path):
+        (tmp_path / "main.py").write_text("print('hello')")
+        (tmp_path / "bad.py").write_text("import unused_module\nx=1")
+
+        from linter_runner import detect_languages, run_linters_for_language
+
+        langs = detect_languages(tmp_path)
+        assert "python" in langs
+
+        result = run_linters_for_language("python", langs["python"][:1], tmp_path)
+        assert result.language == "python"
+        assert result.violations or result.error  # either linter output or not-installed
+
+    def test_json_output_structure(self, tmp_path: Path):
+        (tmp_path / "script.py").write_text("print(1)")
+
+        from linter_runner import detect_languages, run_linters_for_language, _result_to_dict
+
+        langs = detect_languages(tmp_path)
+        if "python" not in langs:
+            pytest.skip("No Python files detected")
+
+        result = run_linters_for_language("python", langs["python"], tmp_path)
+        report = {
+            "repo": tmp_path.name,
+            "languages": {"python": _result_to_dict(result)},
+            "summary": {
+                "total_issues": len(result.violations),
+                "errors": sum(1 for v in result.violations if v.severity == "error"),
+            },
+        }
+        json.dumps(report)  # should not raise
+
+
+if __name__ == "__main__":
+    print("Run: pytest tests/test_linter_runner.py -v")
+