@codeyam/codeyam-cli 0.1.0-staging.6e699e5 → 0.1.0-staging.73a4bf4

package/codeyam-cli/templates/rules-instructions.md

@@ -0,0 +1,132 @@
+# Claude Rules Guide
+
+Rules provide context-specific guidance when working in files matching their `paths` patterns.
+
+## Core Principles
+
+1. **One concept per rule** - Each rule should cover a single topic. If you're documenting two unrelated things, create two rules.
+2. **Paths must match content scope** - A rule about one specific file should have that file in `paths`, not a broad `**/*.ts` pattern.
+3. **Keep rules SHORT** - Most rules should be **1-4 bullets**. Only complex multi-file architectural overviews should exceed ~10 lines. Every word costs context.
+
+### Good vs Bad Rule Length
+
+**Good** — a typical rule (4 bullets):
+
+```markdown
+---
+paths:
+  - 'packages/ai/src/lib/generateMockData.ts'
+---
+
+# Mock Data Generation
+
+- Entry point: `generateMockData()` in `generateMockData.ts`
+- Uses `convertDotNotation` to transform flat schema into nested objects
+- Schema entry ORDER matters — `key[]` must come before `key[].property` or arrays get overwritten
+- Test with exact ordering from database, not just same entries
+```
+
+**Bad** — same info bloated to 40+ lines with unnecessary headers, restating what the code says, and paragraphs instead of bullets.
+
+## When to Create a New Rule
+
+Create a new rule when:
+
+- You learn something non-obvious about the codebase
+- You make a mistake and want to prevent it in the future
+- The user explains something that isn't clear from the code
+- An existing rule is covering multiple unrelated topics (split it)
+
+## Before Creating: What Makes a Rule Valuable?
+
+A rule earns its place when it meets these criteria:
+
+1. **Beyond the code** — It captures knowledge that reading the source alone wouldn't reveal (historical context, non-obvious interactions, gotchas).
+2. **Explains "why" over "what"** — Gotchas, non-obvious behavior, architectural decisions. (Function signatures, bug fixes, and limitations are already visible in code.)
+3. **Prevents real mistakes** — It would have saved someone from a past confusion or bug, not just a "nice to know."
+
+### Examples
+
+**✅ Worth documenting:**
+
+- Where to add new functionality
+- An overview of all files, classes, functions, etc used in a particular part of the repo
+- Debugging strategies for a particular area of the repo
+- "Use `pnpm test` to run tests" (if there is more than one way to run tests and this way is preferred)
+
+Skip things like "The auth module handles authentication" or "This function takes X and returns Y" — Claude can read the code and infer these.
+
+## Path Specificity
+
+The `paths` field controls when the rule is shown. Match the scope of your content:
+
+| Content Scope | Path Pattern            | Example                                                |
+| ------------- | ----------------------- | ------------------------------------------------------ |
+| Single file   | `'path/to/file.ts'`     | Rule about `processExpression.ts` specifically         |
+| Related files | `'path/to/feature*.ts'` | Rule about `generateExecutionFlows*.ts` files          |
+| Directory     | `'path/to/dir/**/*.ts'` | Rule about the queue system in `utils/queue/`          |
+| Cross-cutting | Multiple specific paths | Testing rule with paths to test configs and test files |
+
+Match path specificity to content scope — use `'path/to/feature.ts'` for a single-feature rule, not `'**/*.ts'`.
+
+## File Placement
+
+Place each rule at the **deepest common directory** shared by all its `paths` entries:
+
+1. Take all paths from the rule's frontmatter
+2. Strip filenames — keep only the directory portions
+3. Find the longest shared directory prefix
+4. Place the rule `.md` file in `.claude/rules/<that-prefix>/`
+
+| Paths in frontmatter                                       | Deepest common dir     | Rule location                                  |
+| ---------------------------------------------------------- | ---------------------- | ---------------------------------------------- |
+| `packages/ai/src/lib/foo.ts`, `packages/ai/src/lib/bar.ts` | `packages/ai/src/lib/` | `.claude/rules/packages/ai/src/lib/foo-bar.md` |
+| `packages/ai/src/lib/a.ts`, `packages/ai/src/utils/b.ts`   | `packages/ai/src/`     | `.claude/rules/packages/ai/src/a-and-b.md`     |
+| `packages/ai/**`, `packages/types/**`                      | `packages/`            | `.claude/rules/packages/ai-types.md`           |
+| `src/api/auth.ts` (single file)                            | `src/api/`             | `.claude/rules/src/api/auth.md`                |
+
+Reserve the top level of `.claude/rules/` for rules whose paths genuinely span the entire repo.
+
+## Required Frontmatter
+
+```yaml
+---
+paths:
+  - 'specific/path/to/file.ts'
+  - 'another/specific/path/*.ts'
+---
+```
+
+| Field   | Purpose                                                          |
+| ------- | ---------------------------------------------------------------- |
+| `paths` | Glob patterns - be specific to avoid loading rules unnecessarily |
+
+**Note:** Audit dates live in `.claude/codeyam-rule-state.json` (managed by `codeyam memory touch`). Keep rule frontmatter limited to `paths`.
+
+## Content Guidelines
+
+### Be Actionable
+
+- Good: "Run `pnpm test:api` for API tests"
+- Bad: "Make sure to run the appropriate tests"
+
+### Focus on What to Do
+
+- "Auth tokens are stored in httpOnly cookies via `src/auth/cookies.ts`" tells the reader exactly where to look and what pattern to follow.
+
+## Categories
+
+**architecture** - Design decisions, file relationships, data flow
+
+- "These three files must change together because..."
+- "Data flows from X → Y → Z"
+
+**testing** - Test commands, mock patterns, fixtures
+
+- "Run tests with: `pnpm test path/to/test.ts`"
+- "Must run `pnpm pretest` first because..."
+
+**faq** - Gotchas, workarounds, common questions
+
+- "If you see error X, it means Y"
+- "This looks wrong but is intentional because..."

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@codeyam/codeyam-cli",
-  "version": "0.1.0-staging.6e699e5",
+  "version": "0.1.0-staging.73a4bf4",
   "description": "Local development CLI for CodeYam analysis",
   "type": "module",
   "bin": {
@@ -10,24 +10,24 @@
     "postinstall": "node ./scripts/finalize-analyzer.cjs"
   },
   "dependencies": {
-    "@anthropic-ai/claude-code": "^2.0.76",
-    "@anthropic-ai/sdk": "^0.71.0",
+    "@anthropic-ai/claude-code": "^2.1.7",
+    "@anthropic-ai/sdk": "^0.74.0",
     "@aws-sdk/client-dynamodb": "^3.956.0",
     "@aws-sdk/s3-request-presigner": "^3.940.0",
-    "@aws-sdk/util-dynamodb": "^3.902.0",
-    "@modelcontextprotocol/sdk": "^1.25.2",
+    "@aws-sdk/util-dynamodb": "^3.971.0",
+    "@modelcontextprotocol/sdk": "^1.26.0",
     "@octokit/auth-app": "^8.1.0",
     "@octokit/request": "^10.0.3",
     "@octokit/rest": "^22.0.0",
-    "@react-router/express": "^7.11.0",
+    "@react-router/express": "^7.13.0",
     "@react-router/node": "^7.11.0",
-    "react-router": "^7.12.0",
+    "react-router": "^7.13.0",
     "@sendgrid/mail": "^8.1.4",
     "@supabase/supabase-js": "2.88.0",
     "better-sqlite3": "^12.4.1",
     "chalk": "^5.6.2",
     "chokidar": "^4.0.3",
-    "cli-spinners": "^3.3.0",
+    "cli-spinners": "^3.4.0",
     "domhandler": "^5.0.3",
     "dotenv": "^17.2.3",
     "express": "^5.2.1",
@@ -38,24 +38,26 @@
     "jsdom": "^27.4.0",
     "json5": "^2.2.3",
     "jsonc-parser": "^3.2.1",
-    "kysely": "^0.28.5",
-    "lru-cache": "^11.2.4",
+    "kysely": "^0.28.11",
+    "lru-cache": "^11.2.5",
     "lucide-react": "^0.556.0",
+    "minimatch": "^10.0.1",
     "openai": "^6.16.0",
     "p-queue": "^8.1.0",
     "p-retry": "^7.1.1",
     "pg": "^8.16.3",
     "piscina": "^5.1.4",
     "pixelmatch": "^5.3.0",
-    "playwright": "^1.56.1",
+    "playwright": "1.58.0",
     "pluralize": "^8.0.0",
     "prompts": "^2.4.2",
     "react": "^19.2.3",
-    "react-diff-viewer-continued": "^4.0.6",
+    "react-diff-viewer-continued": "4.0.6",
     "react-dom": "^19.2.3",
     "react-markdown": "^10.1.0",
     "react-resizable": "^3.0.5",
-    "react-syntax-highlighter": "^15.6.1",
+    "react-syntax-highlighter": "^16.1.0",
+    "remark-gfm": "^4.0.1",
     "sharp": "^0.34.5",
     "simple-git": "^3.28.0",
     "typescript": "^5.9.3",

package/packages/ai/index.js

@@ -26,14 +26,15 @@ export { default as describeCodeChange } from "./src/lib/describeCodeChange.js";
 export { default as validateTypeStructure } from "./src/lib/validateTypeStructure.js";
 export { default as validateDataStructure } from "./src/lib/validateDataStructure.js";
 export { default as isolateScopes } from "./src/lib/isolateScopes.js";
-export { default as analyzeScope } from "./src/lib/analyzeScope.js";
+export { default as analyzeScope, destroyWorkerPool, skipWorkerPool, } from "./src/lib/analyzeScope.js";
 export { default as logOrderedMap } from "./src/lib/logOrderedMap.js";
 export { default as splitOutsideParentheses, splitOutsideParenthesesAndArrays, joinParenthesesAndArrays, functionArguments, } from "./src/lib/splitOutsideParentheses.js";
 export { cleanKnownObjectFunctionsFromMapping } from "./src/lib/dataStructure/helpers/cleanKnownObjectFunctions.js";
 export { clearAttributesFromMapping, removeDuplicateFunctionCalls, } from "./src/lib/dataStructure/helpers/cleanNonObjectFunctions.js";
 export { default as convertDotNotation } from "./src/lib/dataStructure/helpers/convertDotNotation.js";
+export { default as convertTypeAnnotationsToValues } from "./src/lib/dataStructure/helpers/convertTypeAnnotationsToValues.js";
 export { default as cleanOutBoundary } from "./src/lib/cleanOutBoundary.js";
-export { fillInDirectSchemaGapsAndUnknowns } from "./src/lib/dataStructure/helpers/fillInSchemaGapsAndUnknowns.js";
+export { fillInDirectSchemaGapsAndUnknowns, buildSchemaIndexes, } from "./src/lib/dataStructure/helpers/fillInSchemaGapsAndUnknowns.js";
 export { default as deduplicateFunctionSchemas } from "./src/lib/dataStructure/helpers/deduplicateFunctionSchemas.js";
 export { default as getConditionalUsagesFromCode } from "./src/lib/getConditionalUsagesFromCode.js";
 export { getExternalFunctionCallInfo, getFunctionSignature, getReturnValue, getUsageEquivalencies, getSourceEquivalencies, getEquivalentSignatureVariables, getConditionalUsages, getConditionalEffects, getCompoundConditionals, getChildBoundaryGatingConditions, getJsxRenderingUsages, } from "./src/lib/worker/SerializableDataStructure.js";

package/packages/ai/index.js.map

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package/packages/ai/src/lib/analyzeScope.js

@@ -34,6 +34,19 @@ import { isMainThread } from 'worker_threads';
 import fs from 'fs';
 // Worker pool for offloading analyzeScope to worker threads
 let workerPool = null;
+let workerPoolDestroyed = false;
+let workerPoolSkipped = false;
+/**
+ * Skip worker pool initialization for the current session.
+ *
+ * The worker thread creates its own ProjectAnalyzer (ts.Program), which takes
+ * 50-70s — far longer than the actual entity processing (<2s for typical batches).
+ * When the entity count is small, running analyzeScopeLocal on the main thread
+ * reuses the existing ProjectAnalyzer and avoids this overhead entirely.
+ */
+export function skipWorkerPool() {
+    workerPoolSkipped = true;
+}
 /**
  * Check if we're in Node.js main thread
  * Returns true for browser environments (where workers don't apply)
@@ -46,11 +59,44 @@ function getIsMainThread() {
     }
     return isMainThread;
 }
+/**
+ * Destroy the worker pool, freeing its ~2GB heap.
+ * Called after data structure preparation completes (the producing phase transition).
+ * The worker is not needed after this point — subsequent calls to ensureWorkerPool() will throw.
+ */
+export async function destroyWorkerPool() {
+    if (workerPool) {
+        const memBefore = process.memoryUsage();
+        console.log('CodeYam: Destroying worker pool...', {
+            rssBefore: `${Math.round(memBefore.rss / 1024 / 1024)}MB`,
+            heapBefore: `${Math.round(memBefore.heapUsed / 1024 / 1024)}MB`,
+        });
+        await workerPool.destroy();
+        workerPool = null;
+        // Force GC if available to reclaim worker memory faster
+        if (global.gc) {
+            global.gc();
+        }
+        const memAfter = process.memoryUsage();
+        console.log('CodeYam: Worker pool destroyed', {
+            rssAfter: `${Math.round(memAfter.rss / 1024 / 1024)}MB`,
+            heapAfter: `${Math.round(memAfter.heapUsed / 1024 / 1024)}MB`,
+            rssDelta: `${Math.round((memAfter.rss - memBefore.rss) / 1024 / 1024)}MB`,
+        });
+    }
+    workerPoolDestroyed = true;
+}
 /**
  * Lazy initialization of worker pool.
  * Called on first use to ensure environment variables are set.
  */
 function ensureWorkerPool() {
+    if (workerPoolDestroyed) {
+        throw new Error('CodeYam: Worker pool was destroyed (post-producing phase). ' +
+            'analyzeScope should not be called after data structure preparation completes.');
+    }
+    if (workerPoolSkipped)
+        return;
     if (workerPool !== null)
         return;
     // Only initialize worker pool in Node.js environment
@@ -62,9 +108,14 @@ function ensureWorkerPool() {
     }
     // Note: WORKER_PATH is null when __mocks__/analyzeScope.ts is active
     const { WORKER_PATH } = analyzeScopeWorkerPaths();
+    // Disable workers when tracing is enabled - we need access to ScopeDataStructure
+    // instance in the main thread to capture pre-serialization state
+    const tracingEnabled = process.env.CODEYAM_TRACE_TRANSFORMS === '1' ||
+        process.env.CODEYAM_TRACE_TRANSFORMS === 'true';
     if (process.env.USE_WORKER_THREADS &&
         WORKER_PATH &&
-        fs.existsSync(WORKER_PATH)) {
+        fs.existsSync(WORKER_PATH) &&
+        !tracingEnabled) {
         console.log('CodeYam: Using worker threads for analyzeScope', {
             WORKER_PATH,
         });
@@ -92,6 +143,7 @@ function ensureWorkerPool() {
             WORKER_PATH,
             workerExists: WORKER_PATH ? fs.existsSync(WORKER_PATH) : false,
             USE_WORKER_THREADS: process.env.USE_WORKER_THREADS,
+            tracingEnabled,
         });
         workerPool = null; // Explicitly set to indicate "no workers"
     }
@@ -228,7 +280,7 @@ export async function analyzeScopeLocal({ entity, fileAnalyzer, scope, scopeData
                     }, null, 2));
                 }
                 for (const mapping of [structure, equivalentVariables]) {
-                    for (let [key, value] of Object.entries(mapping)) {
+                    for (let [key, rawValue] of Object.entries(mapping)) {
                         for (const [childScopeId, childScope] of sortedEntries) {
                             const scopeText = fileAnalyzer.sourceFile.text.slice(childScope.start, childScope.end);
                             const replaceChildScopeId = (text) => {
@@ -243,18 +295,35 @@ export async function analyzeScopeLocal({ entity, fileAnalyzer, scope, scopeData
                                 }
                                 return text;
                             };
-                            if (value.includes(scopeText)) {
-                                // DEBUG: Log when replacement happens
-                                if (key.includes('Fetcher') || key.includes('fetcher')) {
-                                    console.log('CodeYam DEBUG value replacement:', JSON.stringify({
-                                        key,
-                                        oldValue: value,
-                                        childScopeId,
-                                        scopeTextPreview: scopeText.slice(0, 50),
-                                    }));
+                            // Handle both string and string[] values (for OR expressions)
+                            const processValue = (value) => {
+                                if (value.includes(scopeText)) {
+                                    // DEBUG: Log when replacement happens
+                                    if (key.includes('Fetcher') || key.includes('fetcher')) {
+                                        console.log('CodeYam DEBUG value replacement:', JSON.stringify({
+                                            key,
+                                            oldValue: value,
+                                            childScopeId,
+                                            scopeTextPreview: scopeText.slice(0, 50),
+                                        }));
+                                    }
+                                    return replaceChildScopeId(value);
+                                }
+                                return value;
+                            };
+                            if (Array.isArray(rawValue)) {
+                                const newValues = rawValue.map(processValue);
+                                mapping[key] =
+                                    newValues;
+                                rawValue = newValues;
+                            }
+                            else if (typeof rawValue === 'string') {
+                                const newValue = processValue(rawValue);
+                                if (newValue !== rawValue) {
+                                    mapping[key] =
+                                        newValue;
+                                    rawValue = newValue;
                                 }
-                                value = replaceChildScopeId(value);
-                                mapping[key] = value;
                             }
                             if (key.includes(scopeText)) {
                                 const oldKey = key;

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package/packages/ai/src/lib/astScopes/astScopeAnalyzer.js

@@ -197,6 +197,7 @@ export class ASTScopeAnalyzer {
             statementInfo: this.statementInfo,
             typeChecker: this.fileAnalyzer.typeChecker,
             addEquivalence: (leftSide, rightSide) => this.addEquivalence(leftSide, rightSide),
+            addMultipleEquivalencies: (leftSide, rightSides) => this.addMultipleEquivalencies(leftSide, rightSides),
             addType: (path, type) => this.addType(path, type),
             addEnvironmentVariable: (variablePath) => this.addEnvironmentVariable(variablePath),
             markUnsupported: (node, message, isBlocking) => this.markUnsupported(node, message, isBlocking),
@@ -487,7 +488,9 @@ export class ASTScopeAnalyzer {
             nodeToSource(node, this.sourceFile));
     }
     /**
-     * Adds an equivalence relationship between two variable paths
+     * Adds an equivalence relationship between two variable paths.
+     * Uses overwrite semantics - if an equivalence already exists, the new value replaces it
+     * (unless the new value is 'undefined' or 'null').
      */
     addEquivalence(leftSide, rightSide) {
         // Skip adding equivalences if left side is a literal path.
@@ -509,6 +512,33 @@ export class ASTScopeAnalyzer {
             this.equivalentVariables[leftSideStr] = rightSideStr;
         }
     }
+    /**
+     * Adds multiple equivalence relationships for a single variable path.
+     * Used for OR expressions like `x = a || b` where x is equivalent to both a and b.
+     * The values are stored as an array to track all possible sources.
+     */
+    addMultipleEquivalencies(leftSide, rightSides) {
+        if (leftSide?.isLiteral()) {
+            return;
+        }
+        const leftSideStr = leftSide?.toLeftHandSideString();
+        if (!leftSideStr)
+            return;
+        // Filter out invalid paths and convert to strings
+        const validRightSides = rightSides
+            .map((r) => r?.toRightHandSideString())
+            .filter((r) => !!r && r !== leftSideStr);
+        // Remove duplicates while preserving order
+        const uniqueRightSides = [...new Set(validRightSides)];
+        // Filter out 'undefined' and 'null' unless they're the only values
+        const meaningfulValues = uniqueRightSides.filter((v) => v !== 'undefined' && v !== 'null');
+        const finalValues = meaningfulValues.length > 0 ? meaningfulValues : uniqueRightSides;
+        if (finalValues.length === 0)
+            return;
+        // Store as single value if only one, otherwise as array
+        this.equivalentVariables[leftSideStr] =
+            finalValues.length === 1 ? finalValues[0] : finalValues;
+    }
     /**
      * Adds a type for a variable path
      */
@@ -628,19 +658,35 @@ export class ASTScopeAnalyzer {
         const pathStr = path.toString();
         // Update the type for the given path
         this.structure[pathStr] = newType;
-        // Also update the type for any equivalent path
+        // Also update the type for any equivalent path(s)
         // e.g., if "state" -> "signature[0]", update "signature[0]" as well
-        const equivalentPath = this.equivalentVariables[pathStr];
-        if (equivalentPath) {
-            this.structure[equivalentPath] = newType;
+        const rawEquivalentPath = this.equivalentVariables[pathStr];
+        const equivalentPaths = Array.isArray(rawEquivalentPath)
+            ? rawEquivalentPath
+            : rawEquivalentPath
+                ? [rawEquivalentPath]
+                : [];
+        for (const equivalentPath of equivalentPaths) {
+            if (typeof equivalentPath === 'string') {
+                this.structure[equivalentPath] = newType;
+            }
         }
         // For property paths like "data.status", check if the base has an equivalence
         // e.g., if "data" -> "signature[0]", transform "data.status" to "signature[0].status"
-        for (const [varPath, equivalence] of Object.entries(this.equivalentVariables)) {
+        for (const [varPath, rawEquivalence] of Object.entries(this.equivalentVariables)) {
             if (pathStr.startsWith(varPath + '.')) {
+                const equivalences = Array.isArray(rawEquivalence)
+                    ? rawEquivalence
+                    : rawEquivalence
+                        ? [rawEquivalence]
+                        : [];
                 const suffix = pathStr.slice(varPath.length);
-                const transformedPath = equivalence + suffix;
-                this.structure[transformedPath] = newType;
+                for (const equivalence of equivalences) {
+                    if (typeof equivalence === 'string') {
+                        const transformedPath = equivalence + suffix;
+                        this.structure[transformedPath] = newType;
+                    }
+                }
             }
         }
     }