codesift-mcp 0.3.0 → 0.5.0

package/dist/tools/hono-security.js

@@ -0,0 +1,269 @@
+/**
+ * audit_hono_security — security + type-safety audit of Hono application.
+ *
+ * Checks:
+ *   - missing-secure-headers (global)
+ *   - missing-rate-limit (mutation routes, conditional-aware)
+ *   - missing-auth (mutation routes, conditional-aware)
+ *   - auth-ordering (auth after non-auth in a chain)
+ *   - env-regression (plain createMiddleware in 3+ chains, Issue #3587)
+ *     — absorbed from the former detect_middleware_env_regression tool.
+ *       It is a type-safety check that still walks middleware chains,
+ *       so it fits the audit surface.
+ *
+ * Spec: docs/specs/2026-04-10-hono-framework-intelligence-spec.md (Task 21) +
+ *       docs/specs/2026-04-11-hono-phase-2-plan.md (T10 consolidation)
+ */
+import { getCodeIndex } from "./index-tools.js";
+import { honoCache } from "../cache/hono-cache.js";
+import { HonoExtractor } from "../parser/extractors/hono.js";
+import { resolveHonoEntryFile } from "./hono-entry-resolver.js";
+import { detectFrameworks } from "../utils/framework-detect.js";
+import { readFile } from "node:fs/promises";
+import { existsSync } from "node:fs";
+import { join, dirname, resolve as pathResolve } from "node:path";
+const RATE_LIMIT_KEYWORDS = /rate\s*limit/i;
+const SECURE_HEADERS_KEYWORDS = /secure[_-]?headers/i;
+const AUTH_KEYWORDS = /auth|jwt|bearer|clerk|session/i;
+const MUTATION_METHODS = new Set(["POST", "PUT", "DELETE", "PATCH"]);
+/**
+ * Regex explanation:
+ *   \bcreateMiddleware   → word-boundary before the token
+ *   (?!\s*<)             → negative lookahead — NOT followed by `<` (generic arg)
+ *   \s*\(                → open paren of the call
+ *
+ * Matches:  createMiddleware(async (c, next) => ...)
+ * Does not match:  createMiddleware<AppEnv>(...)
+ */
+const PLAIN_CREATE_MIDDLEWARE = /\bcreateMiddleware(?!\s*<)\s*\(/g;
+const ENV_REGRESSION_NOTE = "env-regression is a heuristic regex scan; false positives possible when middleware factories wrap createMiddleware or re-export it under a different name. Review each finding before typing changes.";
+/**
+ * Does a conditional middleware apply to a given HTTP method?
+ *
+ * Phase 2 T4 populates `applied_when` on inline-gated middleware like
+ *
+ *     app.use('/posts/*', async (c, next) => {
+ *       if (c.req.method !== 'GET') return basicAuth({...})(c, next);
+ *       await next();
+ *     });
+ *
+ * Without this check the auditor reports "missing auth" on POST /posts even
+ * though the route IS gated. We inspect condition_text for method equality
+ * patterns and decide whether the conditional entry covers the method in
+ * question. When we can't tell statically, we default to "applies" (safe
+ * side — no false positive).
+ */
+function conditionalAppliesToMethod(entry, method) {
+    if (!entry.applied_when)
+        return true;
+    if (entry.applied_when.condition_type !== "method")
+        return true;
+    const text = entry.applied_when.condition_text;
+    // Pattern: method !== 'X' (or "X") — middleware runs for anything NOT X
+    const neqMatch = text.match(/method\s*!==?\s*["']([A-Z]+)["']/i);
+    if (neqMatch?.[1])
+        return neqMatch[1].toUpperCase() !== method.toUpperCase();
+    // Pattern: method === 'X' — middleware runs only for X
+    const eqMatch = text.match(/method\s*===?\s*["']([A-Z]+)["']/i);
+    if (eqMatch?.[1])
+        return eqMatch[1].toUpperCase() === method.toUpperCase();
+    return true;
+}
+export async function auditHonoSecurity(repo) {
+    const index = await getCodeIndex(repo);
+    if (!index)
+        return { error: `Repository "${repo}" not found` };
+    const frameworks = detectFrameworks(index);
+    if (!frameworks.has("hono"))
+        return { error: "No Hono app detected" };
+    const entryFile = resolveHonoEntryFile(index);
+    if (!entryFile)
+        return { error: "No Hono entry file found" };
+    let model;
+    try {
+        model = await honoCache.get(repo, entryFile, new HonoExtractor());
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        return { error: `Failed to parse: ${msg}` };
+    }
+    const findings = [];
+    // Check 1: global secure-headers middleware
+    const hasSecureHeaders = model.middleware_chains.some((mc) => mc.scope === "*" &&
+        mc.entries.some((e) => SECURE_HEADERS_KEYWORDS.test(e.name)));
+    if (!hasSecureHeaders) {
+        findings.push({
+            severity: "MEDIUM",
+            rule: "missing-secure-headers",
+            message: "No secure-headers middleware registered globally. Consider `app.use('*', secureHeaders())` from hono/secure-headers.",
+        });
+    }
+    // Check 2: mutation routes without rate limiting.
+    // Phase 2: conditional entries only count if their applied_when covers
+    // the route's method — otherwise a conditional GET-only middleware would
+    // fail to protect a POST route anyway.
+    for (const route of model.routes) {
+        if (!MUTATION_METHODS.has(route.method))
+            continue;
+        const activeChains = model.middleware_chains.filter((mc) => {
+            if (mc.scope === "*")
+                return true;
+            const pattern = mc.scope.replace(/\*/g, ".*");
+            return new RegExp(`^${pattern}$`).test(route.path);
+        });
+        const hasRateLimit = activeChains.some((mc) => mc.entries.some((e) => RATE_LIMIT_KEYWORDS.test(e.name) &&
+            conditionalAppliesToMethod(e, route.method)));
+        if (!hasRateLimit) {
+            findings.push({
+                severity: "HIGH",
+                rule: "missing-rate-limit",
+                message: `Mutation route ${route.method} ${route.path} has no rate limiting middleware.`,
+                file: route.file,
+                line: route.line,
+            });
+        }
+    }
+    // Check 2b: mutation routes without auth. Uses the same conditional-aware
+    // logic so conditional basicAuth like the blog API pattern is recognized.
+    for (const route of model.routes) {
+        if (!MUTATION_METHODS.has(route.method))
+            continue;
+        const activeChains = model.middleware_chains.filter((mc) => {
+            if (mc.scope === "*")
+                return true;
+            const pattern = mc.scope.replace(/\*/g, ".*");
+            return new RegExp(`^${pattern}$`).test(route.path);
+        });
+        const hasAuth = activeChains.some((mc) => mc.entries.some((e) => AUTH_KEYWORDS.test(e.name) &&
+            conditionalAppliesToMethod(e, route.method)));
+        if (!hasAuth) {
+            findings.push({
+                severity: "HIGH",
+                rule: "missing-auth",
+                message: `Mutation route ${route.method} ${route.path} has no auth middleware in its scope.`,
+                file: route.file,
+                line: route.line,
+            });
+        }
+    }
+    // Check 3: auth ordering — auth middleware appearing after non-auth in chain.
+    // Skip <inline> wrappers and conditional entries from the "seenNonAuth"
+    // ordering check: both are structurally different from named middleware
+    // and reporting them as "non-auth" causes false positives on the common
+    // conditional-auth wrapper pattern.
+    for (const mc of model.middleware_chains) {
+        let seenNonAuth = false;
+        for (const entry of mc.entries) {
+            if (entry.name === "<inline>" || entry.applied_when)
+                continue;
+            if (AUTH_KEYWORDS.test(entry.name)) {
+                if (seenNonAuth) {
+                    findings.push({
+                        severity: "MEDIUM",
+                        rule: "auth-ordering",
+                        message: `Auth middleware "${entry.name}" appears after non-auth middleware in scope "${mc.scope}". Auth should be registered first.`,
+                        file: entry.file,
+                        line: entry.line,
+                    });
+                }
+            }
+            else {
+                seenNonAuth = true;
+            }
+        }
+    }
+    // Check 4: env-regression — Hono Issue #3587. Middleware chains of 3+
+    // entries where an intermediate member is declared with plain
+    // `createMiddleware(...)` (no Env generic) reset the accumulated Env
+    // type to BlankEnv for all downstream middleware.
+    // Cache file scans so shared middleware files are only read once.
+    const regressionScanCache = new Map();
+    let emittedEnvRegression = false;
+    for (const chain of model.middleware_chains) {
+        if (chain.entries.length < 3)
+            continue;
+        // Intermediate entries only — first + last are endpoints of the chain.
+        const intermediates = chain.entries.slice(1, -1);
+        for (const entry of intermediates) {
+            if (entry.is_third_party)
+                continue;
+            if (entry.inline)
+                continue;
+            const definitionFile = resolveDefinitionFile(entry.file, entry.imported_from);
+            if (!definitionFile)
+                continue;
+            let hits = regressionScanCache.get(definitionFile);
+            if (!hits) {
+                hits = await scanFileForPlainCreateMiddleware(definitionFile);
+                regressionScanCache.set(definitionFile, hits);
+            }
+            if (hits.length === 0)
+                continue;
+            const first = hits[0];
+            if (!first)
+                continue;
+            emittedEnvRegression = true;
+            findings.push({
+                severity: "MEDIUM",
+                rule: "env-regression",
+                message: `Middleware "${entry.name}" in chain "${chain.scope}" (${chain.entries.length} entries) is declared with plain createMiddleware(...) without an Env generic — this resets the accumulated Env type to BlankEnv for downstream middleware (Hono Issue #3587).`,
+                file: definitionFile,
+                line: first.line,
+            });
+        }
+    }
+    const result = { findings };
+    if (emittedEnvRegression) {
+        result.notes = { "env-regression": ENV_REGRESSION_NOTE };
+    }
+    return result;
+}
+/**
+ * Resolve the definition file for a middleware entry from the caller file and
+ * its import specifier. Returns the absolute path, or null if the import is
+ * third-party or cannot be resolved on disk. Used by the env-regression check.
+ */
+function resolveDefinitionFile(callerFile, importSpec) {
+    if (!importSpec) {
+        return existsSync(callerFile) ? callerFile : null;
+    }
+    if (!importSpec.startsWith(".")) {
+        return null;
+    }
+    const base = pathResolve(dirname(callerFile), importSpec);
+    const candidates = [
+        base,
+        `${base}.ts`,
+        `${base}.tsx`,
+        `${base}.js`,
+        `${base}.jsx`,
+        join(base, "index.ts"),
+        join(base, "index.tsx"),
+        join(base, "index.js"),
+        join(base, "index.jsx"),
+    ];
+    for (const candidate of candidates) {
+        if (existsSync(candidate))
+            return candidate;
+    }
+    return null;
+}
+async function scanFileForPlainCreateMiddleware(file) {
+    let source;
+    try {
+        source = await readFile(file, "utf-8");
+    }
+    catch {
+        return [];
+    }
+    const hits = [];
+    // Reset regex state per scan (global flag retains lastIndex).
+    PLAIN_CREATE_MIDDLEWARE.lastIndex = 0;
+    let m;
+    while ((m = PLAIN_CREATE_MIDDLEWARE.exec(source)) !== null) {
+        const line = source.slice(0, m.index).split("\n").length;
+        hits.push({ line });
+    }
+    return hits;
+}
+//# sourceMappingURL=hono-security.js.map

package/dist/tools/hono-security.js.map

@@ -0,0 +1 @@
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package/dist/tools/hono-visualize.d.ts

@@ -0,0 +1,13 @@
+/**
+ * visualize_hono_routes — produce Mermaid or ASCII tree of Hono routing topology.
+ *
+ * Spec: docs/specs/2026-04-10-hono-framework-intelligence-spec.md (Task 22)
+ */
+export type VisualizeFormat = "mermaid" | "tree";
+export interface VisualizeResult {
+    format?: VisualizeFormat;
+    output?: string;
+    error?: string;
+}
+export declare function visualizeHonoRoutes(repo: string, format?: VisualizeFormat): Promise<VisualizeResult>;
+//# sourceMappingURL=hono-visualize.d.ts.map

package/dist/tools/hono-visualize.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"hono-visualize.d.ts","sourceRoot":"","sources":["../../src/tools/hono-visualize.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,MAAM,MAAM,eAAe,GAAG,SAAS,GAAG,MAAM,CAAC;AAEjD,MAAM,WAAW,eAAe;IAC9B,MAAM,CAAC,EAAE,eAAe,CAAC;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,wBAAsB,mBAAmB,CACvC,IAAI,EAAE,MAAM,EACZ,MAAM,GAAE,eAAwB,GAC/B,OAAO,CAAC,eAAe,CAAC,CAsD1B"}

package/dist/tools/hono-visualize.js

@@ -0,0 +1,64 @@
+/**
+ * visualize_hono_routes — produce Mermaid or ASCII tree of Hono routing topology.
+ *
+ * Spec: docs/specs/2026-04-10-hono-framework-intelligence-spec.md (Task 22)
+ */
+import { getCodeIndex } from "./index-tools.js";
+import { honoCache } from "../cache/hono-cache.js";
+import { HonoExtractor } from "../parser/extractors/hono.js";
+import { resolveHonoEntryFile } from "./hono-entry-resolver.js";
+import { detectFrameworks } from "../utils/framework-detect.js";
+export async function visualizeHonoRoutes(repo, format = "tree") {
+    const index = await getCodeIndex(repo);
+    if (!index)
+        return { error: `Repository "${repo}" not found` };
+    const frameworks = detectFrameworks(index);
+    if (!frameworks.has("hono"))
+        return { error: "No Hono app detected" };
+    const entryFile = resolveHonoEntryFile(index);
+    if (!entryFile)
+        return { error: "No Hono entry file found" };
+    let model;
+    try {
+        model = await honoCache.get(repo, entryFile, new HonoExtractor());
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        return { error: `Failed to parse: ${msg}` };
+    }
+    if (format === "mermaid") {
+        const lines = ["graph LR"];
+        lines.push('  app["Hono app"]');
+        for (const mount of model.mounts) {
+            const id = mount.mount_path.replace(/[^a-zA-Z0-9]/g, "_");
+            lines.push(`  app --> ${id}["${mount.mount_path}"]`);
+        }
+        for (const route of model.routes) {
+            const id = `${route.method}_${route.path.replace(/[^a-zA-Z0-9]/g, "_")}`;
+            lines.push(`  app -.-> ${id}["${route.method} ${route.path}"]`);
+        }
+        return { format, output: lines.join("\n") };
+    }
+    // Tree format (ASCII)
+    const lines = ["Hono Application"];
+    lines.push(`├── runtime: ${model.runtime}`);
+    lines.push(`├── routes (${model.routes.length})`);
+    for (let i = 0; i < model.routes.length; i++) {
+        const route = model.routes[i];
+        const isLast = i === model.routes.length - 1 && model.mounts.length === 0;
+        const prefix = isLast ? "└──" : "├──";
+        lines.push(`│   ${prefix} ${route.method} ${route.path}`);
+    }
+    if (model.mounts.length > 0) {
+        lines.push(`├── mounts (${model.mounts.length})`);
+        for (let i = 0; i < model.mounts.length; i++) {
+            const mount = model.mounts[i];
+            const isLast = i === model.mounts.length - 1;
+            const prefix = isLast ? "└──" : "├──";
+            lines.push(`│   ${prefix} ${mount.mount_path} → ${mount.child_var}`);
+        }
+    }
+    lines.push(`└── middleware chains (${model.middleware_chains.length})`);
+    return { format, output: lines.join("\n") };
+}
+//# sourceMappingURL=hono-visualize.js.map

package/dist/tools/hono-visualize.js.map

@@ -0,0 +1 @@
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package/dist/tools/hotspot-tools.d.ts.map

@@ -1 +1 @@
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package/dist/tools/hotspot-tools.js

@@ -29,14 +29,16 @@ function getGitChurn(repoRoot, sinceDays) {
     for (const line of lines) {
         const trimmed = line.trim();
         if (!trimmed) {
-            // End of a commit's stats — record commit counts
-            for (const file of commitFiles) {
-                const entry = churn.get(file);
-                if (entry)
-                    entry.commits++;
+            // Empty line after numstat lines → end of a commit's stats
+            // Empty line right after hash → skip (git format: hash\n\nnumstat)
+            if (commitFiles.size > 0) {
+                for (const file of commitFiles) {
+                    const entry = churn.get(file);
+                    if (entry)
+                        entry.commits++;
+                }
+                commitFiles.clear();
             }
-            commitFiles.clear();
-            inCommit = false;
             continue;
         }
         // Commit hash line (40 hex chars)

package/dist/tools/hotspot-tools.js.map

@@ -1 +1 @@
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package/dist/tools/index-tools.d.ts

@@ -33,6 +33,7 @@ export interface RepoSummary {
 }
 export declare function listAllRepos(options?: {
     compact?: boolean;
+    name_contains?: string;
 }): Promise<RepoMeta[] | RepoSummary[] | string[]>;
 export declare function invalidateCache(repoName: string): Promise<boolean>;
 /**
@@ -82,4 +83,20 @@ export declare function autoIndexCurrentRepo(cwd: string): Promise<void>;
  * Loads from disk if not cached. Returns null if no embeddings file exists.
  */
 export declare function getEmbeddingCache(repoName: string): Promise<Map<string, Float32Array> | null>;
+export declare const ASTRO_LOCK_FILENAME = "astro-reindex.lock";
+export declare const EXTRACTOR_VERSIONS_FILENAME = "extractor-versions.json";
+export interface AstroReindexResult {
+    reindexed: boolean;
+    files_reindexed?: number;
+    reason: string;
+}
+/**
+ * Check if the stored astro extractor version matches the current one.
+ * If not, re-extract all .astro files with lockfile protection.
+ *
+ * @param dataDir   The data directory (e.g., ~/.codesift or a test tmpdir)
+ * @param repoRoot  The repo root path (for locating .astro files)
+ * @param astroFiles  Relative paths to .astro files in the repo
+ */
+export declare function checkAstroExtractorVersion(dataDir: string, repoRoot: string, astroFiles: string[]): Promise<AstroReindexResult>;
 //# sourceMappingURL=index-tools.d.ts.map

package/dist/tools/index-tools.d.ts.map

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