claude-ex 1.2.0 → 1.4.0

package/README.md

@@ -21,7 +21,140 @@ That's it. Open Claude Code — the MCP server starts automatically and gives Cl
 2. **Computes PageRank** to identify structurally important symbols
 3. **Runs as MCP server** with the SQLite database held open in memory — every query answers in <5ms
 4. **Watches files** for changes and reindexes in <15ms
-5. **Hooks into Claude Code** to inject context before/after edits
+5. **Generates CLAUDE.md** with a development cycle that Claude follows automatically
+
+## What's New in 1.4.0
+
+### Performance Overhaul
+
+Every query is now faster. The entire engine was rewritten for speed:
+
+- **Prepared statement cache** — SQL is compiled once per db connection, not per call. Every MCP tool invocation skips recompilation.
+- **N+1 query elimination** — `getStats` (4 queries → 1), `getModules` (N+1 → 2), `getFileMap` / `getFileMapCompact` (N+1 → 1 via GROUP_CONCAT)
+- **5 new indexes** — `files(path)`, `symbols(file_id, line_start)`, `file_deps(to_file, from_file)`, `symbols(exported, kind)`, `rankings(pagerank DESC)` — eliminates full table scans in hot-path queries
+- **PageRank O(n) per iteration** — dangling node mass is pre-computed instead of O(n^2) inner loop
+- **Import resolution** — uses pre-computed file set (0 `fs.existsSync` calls) instead of 11 syscalls per import
+- **`transparentReview`** — 80 queries → 25 (lightweight code fetch instead of full `getContext` per caller)
+- **Compact JSON** — MCP responses use `JSON.stringify(result)` instead of pretty-printed (30-50% smaller, 2x faster serialization)
+- **Pre-warm on startup** — statement cache + SQLite page cache are warm before the first tool call
+
+### Trigram Search
+
+Substring and fuzzy matching, similar to Cursor's Instant Grep approach:
+
+- New `symbols_trigram` FTS5 table with `tokenize='trigram'` for substring matches on symbol names, qualified names, and signatures
+- **Two-pass search** — FTS5 word-level search first (fast, ranked), trigram fallback if results are sparse
+- **FTS5 prefix index** (`prefix='2 4'`) — 80% faster prefix/autocomplete queries
+- **NEAR phrase queries** — multi-token searches like `"get user"` use `NEAR` operator for better relevance, falling back to `OR` for partial matches
+
+### Development Cycle in CLAUDE.md
+
+The generated CLAUDE.md now includes a mandatory development cycle that Claude follows for every code change:
+
+1. **Understand** — `search_code` → `get_symbol` → `get_callers` → `get_dependents` before touching anything
+2. **Plan** — identify all affected files/symbols, state the plan if >3 files
+3. **Implement** — edit code, update all callers, `reindex_file` after major changes
+4. **Verify** — re-check callers/dependents, run tests and build
+5. **Review** — `review_diff` for graph-aware risk assessment
+
+Each step has a gate condition and a quick-reference table mapping steps to tools. Claude won't skip steps.
+
+### CLAUDE.md Generator Improvements
+
+- **Skip-if-unchanged** — won't rewrite the file if the generated section is identical (no more spurious git diffs)
+- **Marker-safe** — only replaces content between `<!-- claude-ex:start -->` and `<!-- claude-ex:end -->`, preserving all user content before and after
+- **Directive-style MCP docs** — decision guide table tells Claude exactly when to use each tool vs grep
+- **Development cycle** — enforced process section (see above)
+
+### Test Suite
+
+93 tests across 5 files, runnable via `npm test`:
+
+- **`tests/schema.test.ts`** (17) — database creation, tables, indexes, FTS, CRUD operations
+- **`tests/engine.test.ts`** (25) — search, callers, context, impact, stats, file map, type hierarchy, dead exports, package usages
+- **`tests/indexer.test.ts`** (10) — full index, file dependencies, PageRank, re-index, parser integration
+- **`tests/claudemd.test.ts`** (11) — markers, user content preservation, skip-if-unchanged, development cycle
+- **`tests/perf.test.ts`** (18) — performance gates (<50ms per query), data integrity (PageRank sum, no orphans, FTS sync)
+
+### Other Improvements
+
+- **Batch watcher debounce** — burst of file saves → single reindex batch (300ms window)
+- **Memoized tool list** — MCP `ListTools` response allocated once, not per request
+- **Cached insert statements** — `insertSymbol`, `insertEdge`, `insertPkgDep`, etc. use WeakMap-cached prepared statements
+
+## Transparent Review (`transparent_review`)
+
+Zero-black-box code review. Instead of dumping JSON metadata, it produces a **readable English narrative** that shows you exactly what changed and why it matters — no interpretation required.
+
+### Usage
+
+In Claude Code, use the `transparent_review` MCP tool, or from the CLI:
+
+```
+claude-ex transparent-review                Review the last commit
+claude-ex transparent-review staged         Review staged changes
+claude-ex transparent-review branch         Review current branch vs main (PR review)
+claude-ex transparent-review abc1234        Review a specific commit
+```
+
+### What you get
+
+For every changed symbol, the review shows:
+
+1. **Exact before/after code** — the old version is found by name in git history, not by shifted line numbers
+2. **Plain-English description** — "Partially modified. 2 lines added. Added error handling (try/catch). 1 new conditional branch."
+3. **Per-symbol diff snippets** — the actual `+`/`-` lines scoped to that symbol
+4. **Caller impact stories** — which functions in other files call the changed code, their source, and whether they'll break or just see behavior changes
+5. **Blast radius by depth** — direct importers vs 2-3 levels deep, with symbol counts
+6. **Risk assessment** — PageRank importance, cascade risk for widely-used exports, API signature changes, broken imports from deleted files
+
+### Example output
+
+```
+## What Changed (file by file)
+
+### `src/auth/session.ts` — modified
+  +12 / -3 lines
+
+#### `validateToken` — function (exported)
+
+What changed: Partially modified. Signature changed. 1 new parameter(s) added.
+Added error handling (try/catch). 1 new conditional branch.
+
+[Before/After code shown inline]
+[Diff snippet for this symbol]
+
+---
+## Who Gets Affected
+
+2 caller(s) in other files use the changed exports:
+
+- **handleRequest** in `src/routes/api.ts`
+  calls validateToken. Signature changed, so this caller may need updating.
+  [Caller code shown]
+
+---
+## Blast Radius
+
+3 file(s) could be transitively affected:
+
+Direct importers (2 files):
+  - `src/routes/api.ts` (8 symbols)
+  - `src/middleware/auth.ts` (3 symbols)
+
+2 levels deep (1 file):
+  - `src/app.ts` (12 symbols)
+```
+
+### How it differs from `review_diff`
+
+| `review_diff` | `transparent_review` |
+|---|---|
+| Returns structured JSON | Returns readable markdown narrative |
+| Lists changed symbol names | Shows actual before/after code |
+| Lists affected dependents | Explains *how* each caller is affected |
+| Risk flags as strings | Risk assessment with context and reasoning |
+| You need to interpret the data | You read it and understand what happened |
 
 ## Code Review (`/review`)
 
@@ -51,44 +184,55 @@ In Claude Code, type:
    - Cross-file concerns
    - Verdict + action items
 
-### When it helps most
-
-- Multi-file refactors — catches "you changed X but 12 callers need updates"
-- Exported API changes — flags widely-used exports that were modified
-- Large PRs — risk signals help prioritize what to look at
-- Deleted files — warns if something still imports from them
-
 ## MCP Tools
 
 | Tool | What it does | Speed |
 |------|-------------|-------|
-| `search_code` | Hybrid FTS5 + PageRank search | 1-3ms |
-| `get_symbol` | Full context for a symbol | 2-4ms |
-| `get_callers` | Who calls this function | 1-3ms |
-| `get_dependents` | What breaks if a file changes | 2-5ms |
-| `get_dependencies` | What a symbol depends on | 1-3ms |
-| `get_architecture` | Project overview | 3-5ms |
-| `review_diff` | Graph-aware diff review context | 10-50ms |
+| `search_code` | Hybrid FTS5 + trigram + PageRank search | <3ms |
+| `get_symbol` | Full context for a symbol | <4ms |
+| `get_callers` | Who calls this function | <3ms |
+| `get_dependents` | What breaks if a file changes | <5ms |
+| `get_dependencies` | What a symbol depends on | <3ms |
+| `get_file_map` | Every file and its exports | <5ms |
+| `get_file_symbols` | All symbols in a file | <3ms |
+| `find_files` | Find files by glob pattern | <3ms |
+| `find_by_kind` | All classes, interfaces, enums, etc. | <5ms |
+| `get_type_hierarchy` | Subclasses/implementors | <3ms |
+| `find_dead_exports` | Exported symbols nothing imports | <10ms |
+| `get_pkg_usages` | Files importing a given package | <3ms |
+| `get_architecture` | Project overview | <5ms |
+| `reindex_file` | Re-index after edits | <15ms |
+| `review_diff` | Graph-aware diff review (structured JSON) | 10-50ms |
+| `transparent_review` | Zero-black-box review narrative (readable English) | 15-80ms |
 
 ## CLI Commands
 
 ```
-claude-ex init [path]         Index + install config + generate docs
-claude-ex review [target]     Graph-aware diff review (last_commit/staged/branch/SHA)
-claude-ex search <query>      Search symbols
-claude-ex callers <symbol>    Find callers
-claude-ex context <symbol>    Full symbol context
-claude-ex impact <file>       Impact analysis
-claude-ex deps <symbol>       Dependencies
-claude-ex rank                Top symbols by PageRank
-claude-ex modules             Module map
-claude-ex stats               Index statistics
-claude-ex brief               Project summary (SessionStart hook)
-claude-ex pre-edit <file>     Pre-edit context (PreToolUse hook)
-claude-ex post-edit <file>    Post-edit reindex (PostToolUse hook)
-claude-ex generate-docs       Regenerate CLAUDE.md
-claude-ex mcp                 Run as MCP server
-claude-ex uninstall           Remove all config
+claude-ex init [path]                  Index + install config + generate docs
+claude-ex transparent-review [target]  Zero-black-box review (before/after code, English, blast radius)
+claude-ex review [target]              Graph-aware diff review (structured JSON)
+claude-ex search <query>               Search symbols
+claude-ex callers <symbol>             Find callers
+claude-ex context <symbol>             Full symbol context
+claude-ex impact <file>                Impact analysis
+claude-ex deps <symbol>                Dependencies
+claude-ex rank                         Top symbols by PageRank
+claude-ex modules                      Module map
+claude-ex stats                        Index statistics
+claude-ex brief                        Project summary (SessionStart hook)
+claude-ex pre-edit <file>              Pre-edit context (PreToolUse hook)
+claude-ex post-edit <file>             Post-edit reindex (PostToolUse hook)
+claude-ex generate-docs                Regenerate CLAUDE.md
+claude-ex mcp                          Run as MCP server
+claude-ex uninstall                    Remove all config
+```
+
+## Testing
+
+```bash
+npm test              Run all 93 tests
+npm run test:watch    Watch mode
+npm run prepush       Build + test (pre-push validation)
 ```
 
 ## Supported Languages

package/dist/claude/claudemd.js

@@ -88,35 +88,89 @@ function generateClaudeMd(rootDir, db) {
             lines.push(fileMap);
             lines.push('');
         }
+        // MCP tool guidance — directive style so Claude actually uses them
         lines.push('## Codex MCP Tools — USE THESE');
         lines.push('');
         lines.push('This project has a live code index via MCP. **Always prefer these over grep/ripgrep for structural queries.** They are faster, rank-aware, and understand code relationships.');
         lines.push('');
-        lines.push('| Tool | Use for |');
-        lines.push('|------|---------|');
-        lines.push('| `search_code` | Finding symbols by name or description (PageRank-weighted) |');
-        lines.push('| `find_files` | Finding files by name/path pattern (glob-style, e.g. `**/*.test.ts`) |');
-        lines.push('| `get_file_map` | Complete project map — every file and its exports (the "memory") |');
-        lines.push('| `get_symbol` | Full context for a symbol before modifying it |');
-        lines.push('| `get_callers` | Who calls a function — use before renaming/removing |');
-        lines.push('| `get_dependents` | What files break if a file changes |');
-        lines.push('| `get_dependencies` | What a symbol imports/uses |');
-        lines.push('| `get_file_symbols` | All symbols in a file (not just exports) |');
-        lines.push('| `find_by_kind` | Find all classes, interfaces, enums, etc. |');
-        lines.push('| `get_type_hierarchy` | Who extends/implements a class or interface |');
-        lines.push('| `find_dead_exports` | Exported symbols nothing imports (dead code) |');
-        lines.push('| `get_pkg_usages` | What files import from a given npm/pip package |');
-        lines.push('| `get_architecture` | Project overview, top symbols, module map |');
-        lines.push('| `reindex_file` | Re-index a file after major changes |');
-        lines.push('| `review_diff` | Graph-aware diff review context (changed symbols, impact, risks) |');
-        lines.push('');
-        lines.push('**Workflow tips:**');
-        lines.push('- Before editing a function: `get_symbol` + `get_callers` to understand impact');
-        lines.push('- Before refactoring a file: `get_dependents` to know what breaks');
-        lines.push('- To find code: `search_code` first (structural), fall back to grep only for literal strings/regex');
-        lines.push('- To find files: `find_files` with glob patterns (faster than shell find/ls)');
-        lines.push('- After large changes: `reindex_file` to keep the index fresh');
-        lines.push('- Before reviewing a PR: `review_diff` with "branch" for full graph context');
+        lines.push('### When to use which tool');
+        lines.push('');
+        lines.push('**Finding code** — use instead of Grep/Glob:');
+        lines.push('- `search_code` — find symbols by name or description (PageRank-ranked). Use this FIRST for any "where is X" or "find X" query.');
+        lines.push('- `find_files` — find files by glob pattern (e.g. `**/*.test.ts`). Use instead of shell find/ls.');
+        lines.push('- `get_file_map` — full project map with every file and its exports. Use to orient yourself in an unfamiliar codebase.');
+        lines.push('');
+        lines.push('**Before modifying code** — always check impact:');
+        lines.push('- `get_symbol` — full context for a symbol (code, deps, dependents, co-located symbols). Read this before editing any function/class.');
+        lines.push('- `get_callers` — all callers of a function. Check before renaming, changing signatures, or deleting.');
+        lines.push('- `get_dependents` — all files transitively affected if a file changes. Check before refactoring exports.');
+        lines.push('- `get_dependencies` — what a symbol imports/uses.');
+        lines.push('');
+        lines.push('**Understanding structure:**');
+        lines.push('- `get_file_symbols` — all symbols in a file (not just exports).');
+        lines.push('- `find_by_kind` — find all classes, interfaces, enums, etc. across the project.');
+        lines.push('- `get_type_hierarchy` — subclasses/implementors of a class or interface.');
+        lines.push('- `get_pkg_usages` — files that import a given npm package (use before swapping libraries).');
+        lines.push('- `get_architecture` — project overview with top symbols and module dependency map.');
+        lines.push('');
+        lines.push('**Maintenance:**');
+        lines.push('- `find_dead_exports` — exported symbols nothing imports (dead code candidates).');
+        lines.push('- `reindex_file` — re-index a file after major edits to keep results fresh.');
+        lines.push('- `review_diff` — graph-aware diff review: changed symbols, callers, blast radius, risks.');
+        lines.push('');
+        lines.push('### Decision guide');
+        lines.push('');
+        lines.push('| You want to... | Use this | Not this |');
+        lines.push('|---|---|---|');
+        lines.push('| Find a function/class | `search_code` | Grep/ripgrep |');
+        lines.push('| Find files by name | `find_files` | shell find/ls/Glob |');
+        lines.push('| See what a file exports | `get_file_symbols` | Read entire file |');
+        lines.push('| Check who calls X | `get_callers` | Grep for function name |');
+        lines.push('| Understand blast radius | `get_dependents` | Manual file tracing |');
+        lines.push('| Find a literal string/regex | Grep (built-in) | — |');
+        lines.push('');
+        // Development cycle — enforce process automatically
+        lines.push('## Development Cycle — FOLLOW THIS');
+        lines.push('');
+        lines.push('For every code change, follow this cycle. Do not skip steps.');
+        lines.push('');
+        lines.push('### 1. Understand (before touching anything)');
+        lines.push('- Run `search_code` or `get_file_map` to locate the relevant code.');
+        lines.push('- Run `get_symbol` on every function/class you plan to modify — read its full context, dependencies, and dependents.');
+        lines.push('- Run `get_callers` on any function whose signature, behavior, or name will change. Know who depends on it.');
+        lines.push('- Run `get_dependents` on any file whose exports will change. Know the blast radius.');
+        lines.push('- If unfamiliar with the area, run `get_architecture` to see how modules connect.');
+        lines.push('');
+        lines.push('### 2. Plan (decide what to change)');
+        lines.push('- From step 1, you now know: what the code does, who calls it, and what breaks if it changes.');
+        lines.push('- Identify all files and symbols that need updating (not just the primary target — include callers/dependents that must adapt).');
+        lines.push('- If the change affects >3 files or an exported API, state the plan before writing code.');
+        lines.push('');
+        lines.push('### 3. Implement (make the change)');
+        lines.push('- Edit the code. Prefer minimal, targeted changes.');
+        lines.push('- Update all callers/dependents identified in step 2 — do not leave broken references.');
+        lines.push('- After major edits to a file, run `reindex_file` so subsequent queries reflect your changes.');
+        lines.push('');
+        lines.push('### 4. Verify (confirm nothing broke)');
+        lines.push('- Run `get_callers` again on modified symbols — verify every caller still works with the new signature/behavior.');
+        lines.push('- Run `get_dependents` on modified files — verify no import is left broken.');
+        lines.push('- Run tests if they exist (`npm test`, `pytest`, etc.).');
+        lines.push('- If the project has a build step, run it (`npm run build`, `tsc --noEmit`, etc.).');
+        lines.push('');
+        lines.push('### 5. Review (before committing)');
+        lines.push('- Run `review_diff` with target "staged" or "last_commit" to get a graph-aware review of your changes.');
+        lines.push('- Check the risk assessment: high-importance symbols modified, cascade risks, broken imports.');
+        lines.push('- If risks are flagged, go back to step 4 and address them.');
+        lines.push('');
+        lines.push('### Quick reference');
+        lines.push('');
+        lines.push('| Step | Tools | Gate |');
+        lines.push('|---|---|---|');
+        lines.push('| Understand | `search_code`, `get_symbol`, `get_callers`, `get_dependents` | Know the blast radius |');
+        lines.push('| Plan | (your reasoning) | All affected files identified |');
+        lines.push('| Implement | Edit + `reindex_file` | Code written |');
+        lines.push('| Verify | `get_callers`, `get_dependents`, tests, build | No broken refs, tests pass |');
+        lines.push('| Review | `review_diff` | No unaddressed risks |');
         lines.push('');
         lines.push('*Auto-generated by claude-ex. Run `claude-ex generate-docs` to regenerate.*');
         lines.push(MARKER_END);
@@ -130,21 +184,28 @@ function generateClaudeMd(rootDir, db) {
 function writeClaudeMd(rootDir, db) {
     const content = generateClaudeMd(rootDir, db);
     const claudeMdPath = path.join(rootDir, 'CLAUDE.md');
+    let updated;
     if (fs.existsSync(claudeMdPath)) {
         const existing = fs.readFileSync(claudeMdPath, 'utf-8');
-        if (existing.includes(MARKER_START) && existing.includes(MARKER_END)) {
-            // Replace existing section
-            const before = existing.slice(0, existing.indexOf(MARKER_START));
-            const after = existing.slice(existing.indexOf(MARKER_END) + MARKER_END.length);
-            fs.writeFileSync(claudeMdPath, before + content + after);
+        const startIdx = existing.indexOf(MARKER_START);
+        const endIdx = existing.indexOf(MARKER_END);
+        if (startIdx !== -1 && endIdx !== -1) {
+            // Replace only the generated section, preserve everything before/after
+            const before = existing.slice(0, startIdx);
+            const after = existing.slice(endIdx + MARKER_END.length);
+            updated = before + content + after;
         }
         else {
-            // Append
-            fs.writeFileSync(claudeMdPath, existing.trimEnd() + '\n\n' + content + '\n');
+            // No markers yet — append with a blank line separator
+            updated = existing.trimEnd() + '\n\n' + content + '\n';
         }
+        // Skip write if nothing changed
+        if (updated === existing)
+            return;
     }
     else {
-        fs.writeFileSync(claudeMdPath, content + '\n');
+        updated = content + '\n';
     }
+    fs.writeFileSync(claudeMdPath, updated);
 }
 //# sourceMappingURL=claudemd.js.map

package/dist/claude/claudemd.js.map

@@ -1 +1 @@
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