vemora 0.1.0-alpha.15

package/dist/commands/index.js

@@ -0,0 +1,366 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.runIndex = runIndex;
+const chalk_1 = __importDefault(require("chalk"));
+const fs_1 = __importDefault(require("fs"));
+const ora_1 = __importDefault(require("ora"));
+const path_1 = __importDefault(require("path"));
+const config_1 = require("../core/config");
+const factory_1 = require("../embeddings/factory");
+const callgraph_1 = require("../indexer/callgraph");
+const chunker_1 = require("../indexer/chunker");
+const deps_1 = require("../indexer/deps");
+const hasher_1 = require("../indexer/hasher");
+const parser_1 = require("../indexer/parser");
+const scanner_1 = require("../indexer/scanner");
+const todos_1 = require("../indexer/todos");
+const cache_1 = require("../storage/cache");
+const repository_1 = require("../storage/repository");
+async function runIndex(rootDir, options = {}) {
+    const config = (0, config_1.loadConfig)(rootDir);
+    const repo = new repository_1.RepositoryStorage(rootDir);
+    const cacheStorage = new cache_1.EmbeddingCacheStorage(config.projectId);
+    console.log(chalk_1.default.bold(`Indexing ${chalk_1.default.cyan(config.projectName)}...`));
+    console.log();
+    // ── Step 0: Initial full or incremental index ───────────────────────────────
+    const { newFiles, newChunks, newSymbols, newDeps, newCallGraph, newTodos, stats, changedPaths, deletedPaths, } = await performIndexIteration(rootDir, config, repo, options);
+    if (changedPaths.length > 0 || deletedPaths.length > 0) {
+        // Save everything from the initial run
+        repo.saveFiles(newFiles);
+        repo.saveChunks(newChunks);
+        repo.saveSymbols(newSymbols);
+        repo.saveDeps(newDeps);
+        repo.saveCallGraph(newCallGraph);
+        repo.saveTodos(newTodos);
+        if (!options.noEmbed && config.embedding.provider !== "none") {
+            const cache = await generateEmbeddings(newChunks, cacheStorage.load(), config, cacheStorage);
+            await rebuildHNSWIndex(newChunks, cache, cacheStorage);
+        }
+        updateMetadata(repo, config, newFiles, newSymbols, stats, newCallGraph);
+        console.log(chalk_1.default.bold.green("\nInitial indexing complete!"));
+    }
+    else {
+        console.log(chalk_1.default.green("Index is already up to date."));
+    }
+    // ── Step 1: Start watcher if requested ──────────────────────────────────────
+    if (options.watch) {
+        await startWatcher(rootDir, config, repo, cacheStorage, options);
+    }
+}
+/**
+ * Performs a single pass of indexing (scan, hash, parse, deps).
+ * Returns the new state and which paths were affected.
+ */
+async function performIndexIteration(rootDir, config, repo, options, specificPaths) {
+    // Load previous state
+    const prevFiles = options.force ? {} : repo.loadFiles();
+    const prevChunks = options.force ? [] : repo.loadChunks();
+    const prevSymbols = options.force ? {} : repo.loadSymbols();
+    const prevDeps = options.force ? {} : repo.loadDeps();
+    const prevCallGraph = options.force ? {} : repo.loadCallGraph();
+    let changedPaths = [];
+    let deletedPaths = [];
+    let unchangedPaths = [];
+    const allScannedPaths = new Set();
+    if (specificPaths) {
+        // If called from watcher, we already know what changed
+        changedPaths = specificPaths.changed ?? [];
+        deletedPaths = specificPaths.deleted ?? [];
+        // Carry forward everything else from prevFiles
+        const affected = new Set([...changedPaths, ...deletedPaths]);
+        unchangedPaths = Object.keys(prevFiles).filter((p) => !affected.has(p));
+        for (const p of [...changedPaths, ...unchangedPaths])
+            allScannedPaths.add(p);
+    }
+    else {
+        // Standard run: scan everything
+        const scanSpinner = (0, ora_1.default)("Scanning repository files...").start();
+        const scanned = await (0, scanner_1.scanRepository)(config);
+        scanSpinner.succeed(`Found ${chalk_1.default.bold(scanned.length)} files to consider`);
+        const hashSpinner = (0, ora_1.default)("Computing file hashes...").start();
+        for (const file of scanned) {
+            allScannedPaths.add(file.relativePath);
+            try {
+                const hash = (0, hasher_1.hashFile)(file.absolutePath);
+                const prev = prevFiles[file.relativePath];
+                if (prev && prev.hash === hash && !options.force) {
+                    unchangedPaths.push(file.relativePath);
+                }
+                else {
+                    changedPaths.push(file.relativePath);
+                }
+            }
+            catch {
+                /* skip */
+            }
+        }
+        deletedPaths = Object.keys(prevFiles).filter((p) => !allScannedPaths.has(p));
+        hashSpinner.succeed([
+            chalk_1.default.green(`${unchangedPaths.length} unchanged`),
+            chalk_1.default.yellow(`${changedPaths.length} changed/new`),
+            deletedPaths.length > 0
+                ? chalk_1.default.red(`${deletedPaths.length} deleted`)
+                : null,
+        ]
+            .filter(Boolean)
+            .join(", "));
+    }
+    const newFiles = {};
+    // Carry forward unchanged
+    for (const p of unchangedPaths) {
+        if (prevFiles[p])
+            newFiles[p] = prevFiles[p];
+    }
+    const allFilePaths = allScannedPaths;
+    const reprocessPaths = new Set([...changedPaths, ...deletedPaths]);
+    const newSymbols = Object.fromEntries(Object.entries(prevSymbols).filter(([, sym]) => !reprocessPaths.has(sym.file)));
+    const newChunks = prevChunks.filter((c) => !reprocessPaths.has(c.file));
+    // Carry forward todos from unchanged files
+    const prevTodos = options.force ? [] : repo.loadTodos();
+    const newTodos = prevTodos.filter((t) => !reprocessPaths.has(t.file));
+    // Call Graph partials
+    const partialCallGraphs = [];
+    // Carry forward partial call graphs for unchanged files
+    // (This is a simplified approach: we filter the old global graph)
+    const unchangedCallGraph = {};
+    for (const [callerId, data] of Object.entries(prevCallGraph)) {
+        const file = callerId.split(":")[0];
+        if (reprocessPaths.has(file))
+            continue;
+        unchangedCallGraph[callerId] = data;
+    }
+    partialCallGraphs.push(unchangedCallGraph);
+    const changedContents = new Map();
+    if (changedPaths.length > 0) {
+        const parseSpinner = (0, ora_1.default)(`Parsing ${changedPaths.length} files...`).start();
+        let _parseErrors = 0;
+        const BATCH_SIZE = 4;
+        for (let i = 0; i < changedPaths.length; i += BATCH_SIZE) {
+            const batch = changedPaths.slice(i, i + BATCH_SIZE);
+            await Promise.all(batch.map(async (relativePath) => {
+                const absolutePath = path_1.default.join(rootDir, relativePath);
+                try {
+                    if (!fs_1.default.existsSync(absolutePath))
+                        return;
+                    const content = fs_1.default.readFileSync(absolutePath, "utf-8");
+                    const hash = (0, hasher_1.hashBuffer)(content); // avoids re-reading the file
+                    const stats = fs_1.default.statSync(absolutePath);
+                    const symbols = (0, parser_1.parseSymbols)(relativePath, content);
+                    const chunks = (0, chunker_1.chunkFile)(relativePath, content, symbols, config);
+                    const fileSymbols = (0, parser_1.buildSymbolIndex)(relativePath, symbols);
+                    newFiles[relativePath] = {
+                        hash,
+                        size: stats.size,
+                        lastModified: stats.mtime.toISOString(),
+                        chunks: chunks.map((c) => c.id),
+                        symbols: symbols.map((s) => s.name),
+                    };
+                    Object.assign(newSymbols, fileSymbols);
+                    newChunks.push(...chunks);
+                    changedContents.set(relativePath, content);
+                    newTodos.push(...(0, todos_1.extractTodos)(relativePath, content));
+                    // Extract calls for Call Graph
+                    const fileCalls = (0, callgraph_1.extractFileCalls)(relativePath, content, {
+                        symbols: newSymbols,
+                        deps: prevDeps,
+                        allFiles: allFilePaths,
+                    });
+                    partialCallGraphs.push(fileCalls);
+                }
+                catch (_err) {
+                    _parseErrors++;
+                }
+            }));
+        }
+        parseSpinner.succeed(`Parsed ${changedPaths.length} files`);
+    }
+    const aliases = (0, deps_1.loadTsPathAliases)(rootDir);
+    const newDeps = (0, deps_1.updateDependencyGraph)(prevDeps, changedContents, new Set(deletedPaths), allFilePaths, aliases);
+    const stats = (0, deps_1.graphStats)(newDeps);
+    // Build final Call Graph
+    const newCallGraph = (0, callgraph_1.buildGlobalCallGraph)(partialCallGraphs);
+    return {
+        newFiles,
+        newChunks,
+        newSymbols,
+        newDeps,
+        newCallGraph,
+        newTodos,
+        stats,
+        changedPaths,
+        deletedPaths,
+    };
+}
+function updateMetadata(repo, config, files, symbols, stats, callGraph) {
+    let totalCallEdges = 0;
+    if (callGraph) {
+        totalCallEdges = Object.values(callGraph).reduce((acc, data) => acc + data.calls.length, 0);
+    }
+    const meta = {
+        projectId: config.projectId,
+        projectName: config.projectName,
+        lastIndexed: new Date().toISOString(),
+        indexedFiles: Object.keys(files).length,
+        totalChunks: Object.values(files).reduce((acc, f) => acc + f.chunks.length, 0),
+        totalSymbols: Object.keys(symbols).length,
+        totalDepEdges: stats.totalEdges,
+        totalCallEdges,
+        embeddingProvider: config.embedding.provider,
+        embeddingModel: config.embedding.model,
+    };
+    repo.saveMetadata(meta);
+    return meta;
+}
+async function startWatcher(rootDir, config, repo, cacheStorage, options) {
+    const chokidar = require("chokidar");
+    // micromatch is a transitive dependency of fast-glob — always available
+    const micromatch = require("micromatch");
+    // Use a function so that chokidar filters against relative paths the same way
+    // the scanner does, preventing dist/ and .vemora/ writes from feedback-looping.
+    const isIgnored = (absPath) => {
+        const rel = path_1.default.relative(rootDir, absPath);
+        if (!rel || rel.startsWith(".."))
+            return false;
+        return micromatch.isMatch(rel, config.exclude, { dot: true });
+    };
+    const watcher = chokidar.watch(rootDir, {
+        ignored: isIgnored,
+        persistent: true,
+        ignoreInitial: true,
+    });
+    console.log(chalk_1.default.blue("\nWatching for changes... (Ctrl+C to stop)"));
+    const pendingChanges = new Set();
+    const pendingDeletions = new Set();
+    let debounceTimer = null;
+    const triggerIndex = async () => {
+        const changed = Array.from(pendingChanges);
+        const deleted = Array.from(pendingDeletions);
+        pendingChanges.clear();
+        pendingDeletions.clear();
+        process.stdout.write(chalk_1.default.yellow(`\nChange detected, re-indexing ${changed.length + deleted.length} files... `));
+        try {
+            const { newFiles, newChunks, newSymbols, newDeps, newCallGraph, newTodos, stats } = await performIndexIteration(rootDir, config, repo, options, {
+                changed,
+                deleted,
+            });
+            repo.saveFiles(newFiles);
+            repo.saveChunks(newChunks);
+            repo.saveSymbols(newSymbols);
+            repo.saveDeps(newDeps);
+            repo.saveCallGraph(newCallGraph);
+            repo.saveTodos(newTodos);
+            if (!options.noEmbed && config.embedding.provider !== "none") {
+                const cache = cacheStorage.load();
+                const updatedCache = await generateEmbeddings(newChunks, cache, config, cacheStorage);
+                await rebuildHNSWIndex(newChunks, updatedCache, cacheStorage);
+            }
+            updateMetadata(repo, config, newFiles, newSymbols, stats, newCallGraph);
+            process.stdout.write(chalk_1.default.green("Done.\n"));
+        }
+        catch (err) {
+            process.stdout.write(chalk_1.default.red(`Failed: ${err.message}\n`));
+        }
+    };
+    const handleChange = (filePath, isDeleted = false) => {
+        const rel = path_1.default.relative(rootDir, filePath);
+        if (!rel || rel.startsWith(".."))
+            return;
+        // Apply the same include/exclude rules as the scanner to avoid processing
+        // files like compiled dist/ output or editor temp files.
+        const included = micromatch.isMatch(rel, config.include, { dot: false });
+        const excluded = micromatch.isMatch(rel, config.exclude, { dot: true });
+        if (!included || excluded)
+            return;
+        if (isDeleted) {
+            pendingDeletions.add(rel);
+            pendingChanges.delete(rel);
+        }
+        else {
+            pendingChanges.add(rel);
+            pendingDeletions.delete(rel);
+        }
+        if (debounceTimer)
+            clearTimeout(debounceTimer);
+        debounceTimer = setTimeout(triggerIndex, 500);
+    };
+    watcher
+        .on("add", (p) => handleChange(p))
+        .on("change", (p) => handleChange(p))
+        .on("unlink", (p) => handleChange(p, true));
+    // biome-ignore lint/suspicious/noEmptyBlockStatements: intentionally empty — keeps the process alive
+    return new Promise(() => { }); // Keep alive
+}
+// ─── Embedding Generation ─────────────────────────────────────────────────────
+async function generateEmbeddings(chunks, prevCache, config, cacheStorage) {
+    const cachedIds = new Set([
+        ...Object.keys(prevCache?.embeddings ?? {}),
+        ...(prevCache?.chunkIds ?? []),
+    ]);
+    const toEmbed = chunks.filter((c) => !cachedIds.has(c.id));
+    if (toEmbed.length === 0) {
+        console.log(chalk_1.default.green("✓") + " All embeddings already cached");
+        return prevCache;
+    }
+    const spinner = (0, ora_1.default)(`Generating embeddings for ${chalk_1.default.bold(toEmbed.length)} new chunks via ${config.embedding.provider}...`).start();
+    try {
+        const provider = (0, factory_1.createEmbeddingProvider)(config.embedding);
+        // Prefix each chunk with its location so the embedding captures context
+        const texts = toEmbed.map((c) => `file: ${c.file}\nsymbol: ${c.symbol ?? "(none)"}\n\n${c.content}`);
+        const embeddings = await provider.embed(texts);
+        const newEmbeddings = {};
+        for (let i = 0; i < toEmbed.length; i++) {
+            if (embeddings[i]?.length > 0) {
+                newEmbeddings[toEmbed[i].id] = embeddings[i];
+            }
+        }
+        // Build or update the cache
+        const baseCache = prevCache ?? {
+            projectId: config.projectId,
+            embeddingModel: config.embedding.model,
+            dimensions: config.embedding.dimensions,
+            lastUpdated: new Date().toISOString(),
+            embeddings: {},
+        };
+        // Prune stale entries, then add new ones
+        const validIds = new Set(chunks.map((c) => c.id));
+        const pruned = cacheStorage.prune(validIds, baseCache);
+        const updated = cacheStorage.update(newEmbeddings, pruned);
+        spinner.succeed(`Generated ${chalk_1.default.bold(Object.keys(newEmbeddings).length)} embeddings` +
+            ` (cached locally at ~/.vemora-cache/)`);
+        return updated;
+    }
+    catch (err) {
+        spinner.fail(`Embedding generation failed: ${err.message}`);
+        console.log(chalk_1.default.gray("  Keyword search is still available. Fix the provider config and re-run."));
+        return prevCache;
+    }
+}
+async function rebuildHNSWIndex(chunks, cache, cacheStorage) {
+    if (!cache || !cache.vectors || !cache.chunkIds)
+        return;
+    const spinner = (0, ora_1.default)("Building HNSW search index...").start();
+    try {
+        const { HNSW } = require("hnsw");
+        // Create new index
+        // Using default parameters: M=16, efConstruction=200
+        const dimensions = cache.dimensions;
+        const index = new HNSW(16, 200, dimensions, "cosine");
+        const data = cache.chunkIds.map((id, i) => {
+            const offset = i * dimensions;
+            const vector = cache.vectors.subarray(offset, offset + dimensions);
+            return { id: i, vector: Array.from(vector) };
+        });
+        await index.buildIndex(data);
+        // Save to cache
+        cache.hnswIndex = index.toJSON();
+        cacheStorage.save(cache);
+        spinner.succeed(`HNSW index built with ${chalk_1.default.bold(cache.chunkIds.length)} vectors`);
+    }
+    catch (err) {
+        spinner.fail(`HNSW index build failed: ${err.message}`);
+    }
+}
+//# sourceMappingURL=index.js.map

package/dist/commands/index.js.map

@@ -0,0 +1 @@
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package/dist/commands/init-agent.d.ts

@@ -0,0 +1,23 @@
+export type AgentTarget = "claude" | "copilot" | "cursor" | "windsurf" | "gemini";
+export interface InitAgentOptions {
+    agents?: AgentTarget[];
+    force?: boolean;
+    /** Write Claude Code hooks to .claude/settings.json (Claude target only). */
+    hooks?: boolean;
+}
+export declare const MARKER_START = "<!-- vemora:generated:start -->";
+export declare const MARKER_END = "<!-- vemora:generated:end -->";
+export declare const DEFAULT_INSTRUCTIONS = "## Working with this codebase\n\n- **Before reading any file**, check the Key Exports table to locate the symbol.\n- **Before querying**, try `vemora query` first \u2014 open a file only if context is insufficient.\n- **Before deep-diving a file or symbol**, use `vemora focus` \u2014 aggregates impl, deps, callers, tests, and knowledge in one call.\n- **Before modifying a file**, check blast radius: `vemora deps <file> --root . --reverse-depth 2`.\n- **Before renaming a symbol**, check callers: `vemora usages <SymbolName> --root .` (add `--callers-only` for methods).\n- **After changes**, run the build/test command before declaring done.\n- **Scope discipline**: only change what was asked. No refactoring, comments, or improvements beyond the request.\n- **Save non-obvious findings** with `vemora remember` \u2014 decisions, gotchas, patterns. Skip what's obvious from reading the code.\n\n## Session setup\n\n```bash\nvemora brief --root .          # start of session: project overview + critical knowledge\nvemora index --root . --watch  # background terminal: live re-index on file save\nvemora index --root . --no-embed  # or: re-index manually after significant changes\n```\n\n## Quick reference\n\n| Need | Command |\n|---|---|\n| Session start | `brief --root .` |\n| File or symbol deep-dive | `focus <target> --root .` |\n| Concept / how-does-X question | `context --root . --query \"<question>\"` |\n| Fix / refactor / add code | `context --root . --query \"<task>\" --keyword` |\n| Scope to recent changes | `context --root . --query \"...\" --since HEAD~5` |\n| Complex multi-step task | `plan \"<task>\" --root . --confirm --synthesize` |\n| LLM audit (security/bugs/perf) | `audit --root . --type security,bugs` |\n| Zero-LLM static scan | `triage --root . --type bugs,security` |\n| Find unused code | `dead-code --root .` |\n| Output too long | add `--budget 2000` to any command |\n| No embeddings / fast search | add `--keyword` to `query` or `context` |\n| Who imports a file | `deps <file> --root .` |\n| Blast radius of a change | `deps <file> --root . --reverse-depth 3` |\n| Who uses a symbol | `usages <SymbolName> --root .` |\n| Who calls a method | `usages <Method> --root . --callers-only` |\n| Save a finding | `remember \"text\" --root .` |\n";
+export declare function runInitAgent(rootDir: string, options?: InitAgentOptions): Promise<void>;
+export declare function buildGeneratedBlock(_projectName: string, projectOverview: string | null, npmScripts: Record<string, string>, entryPoints: string[], fileSummaries: Record<string, {
+    summary: string;
+}>, exportedSymbols: Array<[string, {
+    type: string;
+    file: string;
+}]>): string;
+/**
+ * Reads npm scripts from package.json in rootDir.
+ * Returns an empty object if no package.json or no scripts field.
+ */
+export declare function detectNpmScripts(rootDir: string): Record<string, string>;
+//# sourceMappingURL=init-agent.d.ts.map

package/dist/commands/init-agent.d.ts.map

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