From f288662b91b9e6e7864172e67ade93619752953a Mon Sep 17 00:00:00 2001 From: Jack Felke Date: Thu, 12 Mar 2026 08:52:38 -0700 Subject: [PATCH] fix: replace run() misuse with shell() across 8 tools MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes #215. The run() helper uses execFileSync('git', args) — no shell, always prepends 'git'. Many tools were passing shell strings with pipes, redirects, non-git commands, or redundant 'git' prefixes, causing silent failures. Changes: - Add shell() helper to lib/git.ts for commands needing pipes/redirects - verify-completion: use shell() for tsc/build/test commands, fs for package.json, array args for git diff - clarify-intent: use shell() for tsc and find commands - session-handoff: use shell() for command -v and gh pr list - audit-workspace: use run() with array args for git diff, shell() for find - sharpen-followup: use run() with array args for git diff/status - enrich-agent-task: use shell() for piped git ls-files and head commands - sequence-tasks: use shell() for piped git ls-files - checkpoint: use run() with array args for git add/reset, shell() for compound commit command - scope-work: use run() with array args for git status/diff, shell() for piped grep commands --- src/lib/git.ts | 27 ++++++++++++++++++++++++++- src/tools/audit-workspace.ts | 7 ++++--- src/tools/checkpoint.ts | 8 ++++---- src/tools/clarify-intent.ts | 6 +++--- src/tools/enrich-agent-task.ts | 14 +++++++------- src/tools/scope-work.ts | 8 ++++---- src/tools/sequence-tasks.ts | 4 ++-- src/tools/session-handoff.ts | 6 +++--- src/tools/sharpen-followup.ts | 16 ++++++++-------- src/tools/verify-completion.ts | 16 +++++++++------- 10 files changed, 70 insertions(+), 42 deletions(-) diff --git a/src/lib/git.ts b/src/lib/git.ts index a32ee3c..cf87c55 100644 --- a/src/lib/git.ts +++ b/src/lib/git.ts @@ -1,7 +1,32 @@ -import { execFileSync } from "child_process"; +import { execFileSync, execSync } from "child_process"; import { PROJECT_DIR } from "./files.js"; import type { RunError } from "../types.js"; +/** + * Run a shell command string (with pipes, redirects, etc.). + * Use this for non-git commands or git commands that need shell features. + * Returns stdout on success, descriptive error string on failure. + */ +export function shell(cmd: string, opts: { timeout?: number } = {}): string { + try { + return execSync(cmd, { + cwd: PROJECT_DIR, + encoding: "utf-8", + timeout: opts.timeout || 10000, + maxBuffer: 1024 * 1024, + stdio: ["pipe", "pipe", "pipe"], + }).trim(); + } catch (e: any) { + const timedOut = e.killed === true || e.signal === "SIGTERM"; + if (timedOut) { + return `[timed out after ${opts.timeout || 10000}ms]`; + } + const output = e.stdout?.trim() || e.stderr?.trim(); + if (output) return output; + return `[command failed: ${cmd} (exit ${e.status ?? "?"})]`; + } +} + /** * Run a git command safely using execFileSync (no shell injection). * Accepts an array of args (preferred) or a string (split on whitespace for backward compat). diff --git a/src/tools/audit-workspace.ts b/src/tools/audit-workspace.ts index d4306bd..cce47e4 100644 --- a/src/tools/audit-workspace.ts +++ b/src/tools/audit-workspace.ts @@ -1,5 +1,5 @@ import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; -import { run } from "../lib/git.js"; +import { run, shell } from "../lib/git.js"; import { readIfExists, findWorkspaceDocs } from "../lib/files.js"; /** Extract top-level work areas from file paths generically */ @@ -36,7 +36,8 @@ export function registerAuditWorkspace(server: McpServer): void { {}, async () => { const docs = findWorkspaceDocs(); - const recentFiles = run("git diff --name-only HEAD~10 2>/dev/null || echo ''").split("\n").filter(Boolean); + const result = run(["diff", "--name-only", "HEAD~10"]); + const recentFiles = (result.startsWith("[") ? "" : result).split("\n").filter(Boolean); const sections: string[] = []; // Doc freshness @@ -75,7 +76,7 @@ export function registerAuditWorkspace(server: McpServer): void { // Check for gap trackers or similar tracking docs const trackingDocs = Object.entries(docs).filter(([n]) => /gap|track|progress/i.test(n)); if (trackingDocs.length > 0) { - const testFilesCount = parseInt(run("find tests -name '*.spec.ts' -o -name '*.test.ts' 2>/dev/null | wc -l").trim()) || 0; + const testFilesCount = parseInt(shell("find tests -name '*.spec.ts' -o -name '*.test.ts' 2>/dev/null | wc -l").trim()) || 0; sections.push(`## Tracking Docs\n${trackingDocs.map(([n]) => { const age = docStatus.find(d => d.name === n)?.ageHours ?? "?"; return `- .claude/${n} — last updated ${age}h ago`; diff --git a/src/tools/checkpoint.ts b/src/tools/checkpoint.ts index e086f01..432a03e 100644 --- a/src/tools/checkpoint.ts +++ b/src/tools/checkpoint.ts @@ -2,7 +2,7 @@ import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; import { writeFileSync, existsSync, mkdirSync } from "fs"; import { join, dirname } from "path"; -import { run, getBranch, getStatus, getLastCommit, getStagedFiles } from "../lib/git.js"; +import { run, shell, getBranch, getStatus, getLastCommit, getStagedFiles } from "../lib/git.js"; import { PROJECT_DIR } from "../lib/files.js"; import { appendLog, now } from "../lib/state.js"; @@ -84,11 +84,11 @@ ${dirty || "clean"} if (commitResult === "no uncommitted changes") { // Stage the checkpoint file too - run(`git add "${checkpointFile}"`); - const result = run(`${addCmd} && git commit -m "${commitMsg.replace(/"/g, '\\"')}" 2>&1`); + run(["add", checkpointFile]); + const result = shell(`${addCmd} && git commit -m "${commitMsg.replace(/"/g, '\\"')}" 2>&1`); if (result.includes("commit failed") || result.includes("nothing to commit")) { // Rollback: unstage if commit failed - run("git reset HEAD 2>/dev/null"); + run(["reset", "HEAD"]); commitResult = `commit failed: ${result}`; } else { commitResult = result; diff --git a/src/tools/clarify-intent.ts b/src/tools/clarify-intent.ts index 32efa3a..f141269 100644 --- a/src/tools/clarify-intent.ts +++ b/src/tools/clarify-intent.ts @@ -1,6 +1,6 @@ import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; -import { run, getBranch, getStatus, getRecentCommits, getDiffFiles, getStagedFiles } from "../lib/git.js"; +import { run, shell, getBranch, getStatus, getRecentCommits, getDiffFiles, getStagedFiles } from "../lib/git.js"; import { findWorkspaceDocs, PROJECT_DIR } from "../lib/files.js"; import { searchSemantic } from "../lib/timeline-db.js"; import { getRelatedProjects } from "../lib/config.js"; @@ -152,10 +152,10 @@ export function registerClarifyIntent(server: McpServer): void { let hasTestFailures = false; if (!area || area.includes("test") || area.includes("fix") || area.includes("ui") || area.includes("api")) { - const typeErrors = run("pnpm tsc --noEmit 2>&1 | grep -c 'error TS' || echo '0'"); + const typeErrors = shell("pnpm tsc --noEmit 2>&1 | grep -c 'error TS' || echo '0'"); hasTypeErrors = parseInt(typeErrors, 10) > 0; - const testFiles = run("find tests -name '*.spec.ts' -maxdepth 4 2>/dev/null | head -20"); + const testFiles = shell("find tests -name '*.spec.ts' -maxdepth 4 2>/dev/null | head -20"); const failingTests = getTestFailures(); hasTestFailures = failingTests !== "all passing" && failingTests !== "no test report found"; diff --git a/src/tools/enrich-agent-task.ts b/src/tools/enrich-agent-task.ts index 236edfa..0ce7d9a 100644 --- a/src/tools/enrich-agent-task.ts +++ b/src/tools/enrich-agent-task.ts @@ -1,6 +1,6 @@ import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; -import { run, getDiffFiles } from "../lib/git.js"; +import { run, shell, getDiffFiles } from "../lib/git.js"; import { PROJECT_DIR } from "../lib/files.js"; import { getConfig, type RelatedProject } from "../lib/config.js"; import { existsSync, readFileSync } from "fs"; @@ -29,11 +29,11 @@ function findAreaFiles(area: string): string { // If area looks like a path, search directly if (area.includes("/")) { - return run(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`); + return shell(`git ls-files -- '${safeArea}*' 2>/dev/null | head -20`); } // Search for area keyword in git-tracked file paths - const files = run(`git ls-files 2>/dev/null | grep -i '${safeArea}' | head -20`); + const files = shell(`git ls-files 2>/dev/null | grep -i '${safeArea}' | head -20`); if (files && !files.startsWith("[command failed")) return files; // Fallback to recently changed files @@ -42,18 +42,18 @@ function findAreaFiles(area: string): string { /** Find related test files for an area */ function findRelatedTests(area: string): string { - if (!area) return run("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10"); + if (!area) return shell("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10"); const safeArea = shellEscape(area.split(/\s+/)[0]); - const tests = run(`git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | grep -i '${safeArea}' | head -10`); - return tests || run("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10"); + const tests = shell(`git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | grep -i '${safeArea}' | head -10`); + return tests || shell("git ls-files 2>/dev/null | grep -E '\\.(spec|test)\\.(ts|tsx|js|jsx)$' | head -10"); } /** Get an example pattern from the first matching file */ function getExamplePattern(files: string): string { const firstFile = files.split("\n").filter(Boolean)[0]; if (!firstFile) return "no pattern available"; - return run(`head -30 '${shellEscape(firstFile)}' 2>/dev/null || echo 'could not read file'`); + return shell(`head -30 '${shellEscape(firstFile)}' 2>/dev/null || echo 'could not read file'`); } // --------------------------------------------------------------------------- diff --git a/src/tools/scope-work.ts b/src/tools/scope-work.ts index 9b5d971..96b7708 100644 --- a/src/tools/scope-work.ts +++ b/src/tools/scope-work.ts @@ -1,7 +1,7 @@ // CATEGORY 1: scope_work — Plans import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; -import { run, getBranch, getRecentCommits, getStatus } from "../lib/git.js"; +import { run, shell, getBranch, getRecentCommits, getStatus } from "../lib/git.js"; import { readIfExists, findWorkspaceDocs, PROJECT_DIR } from "../lib/files.js"; import { searchSemantic } from "../lib/timeline-db.js"; import { getRelatedProjects } from "../lib/config.js"; @@ -93,9 +93,9 @@ export function registerScopeWork(server: McpServer): void { const timestamp = now(); const currentBranch = branch ?? getBranch(); const recentCommits = getRecentCommits(10); - const porcelain = run("git status --porcelain"); + const porcelain = run(["status", "--porcelain"]); const dirtyFiles = parsePortelainFiles(porcelain); - const diffStat = dirtyFiles.length > 0 ? run("git diff --stat") : "(clean working tree)"; + const diffStat = dirtyFiles.length > 0 ? run(["diff", "--stat"]) : "(clean working tree)"; // Scan for relevant files based on task keywords const keywords = task.toLowerCase().split(/\s+/); @@ -128,7 +128,7 @@ export function registerScopeWork(server: McpServer): void { .slice(0, 5); if (grepTerms.length > 0) { const pattern = shellEscape(grepTerms.join("|")); - matchedFiles = run(`git ls-files | head -500 | grep -iE '${pattern}' | head -30`); + matchedFiles = shell(`git ls-files | head -500 | grep -iE '${pattern}' | head -30`); } // Check which relevant dirs actually exist (with path traversal protection) diff --git a/src/tools/sequence-tasks.ts b/src/tools/sequence-tasks.ts index 22dea23..749a0d9 100644 --- a/src/tools/sequence-tasks.ts +++ b/src/tools/sequence-tasks.ts @@ -1,7 +1,7 @@ // CATEGORY 6: sequence_tasks — Sequencing import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; -import { run } from "../lib/git.js"; +import { run, shell } from "../lib/git.js"; import { now } from "../lib/state.js"; import { PROJECT_DIR } from "../lib/files.js"; import { existsSync } from "fs"; @@ -90,7 +90,7 @@ export function registerSequenceTasks(server: McpServer): void { // For locality: infer directories from path-like tokens in task text if (strategy === "locality") { // Use git ls-files with a depth limit instead of find for performance - const gitFiles = run("git ls-files 2>/dev/null | head -1000"); + const gitFiles = shell("git ls-files 2>/dev/null | head -1000"); const knownDirs = new Set(); for (const f of gitFiles.split("\n").filter(Boolean)) { const parts = f.split("/"); diff --git a/src/tools/session-handoff.ts b/src/tools/session-handoff.ts index d199462..6d01428 100644 --- a/src/tools/session-handoff.ts +++ b/src/tools/session-handoff.ts @@ -2,13 +2,13 @@ import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; import { existsSync, readFileSync } from "fs"; import { join } from "path"; -import { run, getBranch, getRecentCommits, getStatus } from "../lib/git.js"; +import { run, shell, getBranch, getRecentCommits, getStatus } from "../lib/git.js"; import { readIfExists, findWorkspaceDocs } from "../lib/files.js"; import { STATE_DIR, now } from "../lib/state.js"; /** Check if a CLI tool is available */ function hasCommand(cmd: string): boolean { - const result = run(`command -v ${cmd} 2>/dev/null`); + const result = shell(`command -v ${cmd} 2>/dev/null`); return !!result && !result.startsWith("[command failed"); } @@ -44,7 +44,7 @@ export function registerSessionHandoff(server: McpServer): void { // Only try gh if it exists if (hasCommand("gh")) { - const openPRs = run("gh pr list --state open --json number,title,headRefName 2>/dev/null || echo '[]'"); + const openPRs = shell("gh pr list --state open --json number,title,headRefName 2>/dev/null || echo '[]'"); if (openPRs && openPRs !== "[]") { sections.push(`## Open PRs\n\`\`\`json\n${openPRs}\n\`\`\``); } diff --git a/src/tools/sharpen-followup.ts b/src/tools/sharpen-followup.ts index db5acaa..18ef4f1 100644 --- a/src/tools/sharpen-followup.ts +++ b/src/tools/sharpen-followup.ts @@ -1,7 +1,7 @@ // CATEGORY 4: sharpen_followup — Follow-up Specificity import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; -import { run } from "../lib/git.js"; +import { run, shell } from "../lib/git.js"; import { now } from "../lib/state.js"; /** Parse git porcelain output into deduplicated file paths, handling renames (R/C) */ @@ -27,14 +27,14 @@ function parsePortelainFiles(output: string): string[] { /** Get recently changed files, safe for first commit / shallow clones */ function getRecentChangedFiles(): string[] { // Try HEAD~1..HEAD, fall back to just staged, then unstaged - const commands = [ - "git diff --name-only HEAD~1 HEAD 2>/dev/null", - "git diff --name-only --cached 2>/dev/null", - "git diff --name-only 2>/dev/null", + const commands: string[][] = [ + ["diff", "--name-only", "HEAD~1", "HEAD"], + ["diff", "--name-only", "--cached"], + ["diff", "--name-only"], ]; const results = new Set(); - for (const cmd of commands) { - const out = run(cmd); + for (const args of commands) { + const out = run(args); if (out) out.split("\n").filter(Boolean).forEach((f) => results.add(f)); if (results.size > 0) break; // first successful source is enough } @@ -87,7 +87,7 @@ export function registerSharpenFollowup(server: McpServer): void { // Gather context to resolve ambiguity const contextFiles: string[] = [...(previous_files ?? [])]; const recentChanged = getRecentChangedFiles(); - const porcelainOutput = run("git status --porcelain 2>/dev/null"); + const porcelainOutput = run(["status", "--porcelain"]); const untrackedOrModified = parsePortelainFiles(porcelainOutput); const allKnownFiles = [...new Set([...contextFiles, ...recentChanged, ...untrackedOrModified])].filter(Boolean); diff --git a/src/tools/verify-completion.ts b/src/tools/verify-completion.ts index 732532f..5c18210 100644 --- a/src/tools/verify-completion.ts +++ b/src/tools/verify-completion.ts @@ -1,8 +1,8 @@ import { z } from "zod"; import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; -import { run, getStatus } from "../lib/git.js"; +import { run, shell, getStatus } from "../lib/git.js"; import { PROJECT_DIR } from "../lib/files.js"; -import { existsSync } from "fs"; +import { existsSync, readFileSync } from "fs"; import { join } from "path"; /** Detect package manager from lockfiles */ @@ -34,7 +34,9 @@ function detectTestRunner(): string | null { /** Check if a build script exists in package.json */ function hasBuildScript(): boolean { try { - const pkg = JSON.parse(run("cat package.json 2>/dev/null")); + const pkgPath = join(PROJECT_DIR, "package.json"); + if (!existsSync(pkgPath)) return false; + const pkg = JSON.parse(readFileSync(pkgPath, "utf-8")); return !!pkg?.scripts?.build; } catch { return false; } } @@ -55,7 +57,7 @@ export function registerVerifyCompletion(server: McpServer): void { const checks: { name: string; passed: boolean; detail: string }[] = []; // 1. Type check (single invocation, extract both result and count) - const tscOutput = run(`${pm === "npx" ? "npx" : pm} tsc --noEmit 2>&1 | tail -20`); + const tscOutput = shell(`${pm === "npx" ? "npx" : pm} tsc --noEmit 2>&1 | tail -20`); const errorLines = tscOutput.split("\n").filter(l => /error TS\d+/.test(l)); const typePassed = errorLines.length === 0; checks.push({ @@ -80,7 +82,7 @@ export function registerVerifyCompletion(server: McpServer): void { // 3. Tests if (!skip_tests) { const runner = detectTestRunner(); - const changedFiles = run("git diff --name-only HEAD~1 2>/dev/null").split("\n").filter(Boolean); + const changedFiles = run(["diff", "--name-only", "HEAD~1"]).split("\n").filter(Boolean); let testCmd = ""; if (runner === "playwright") { @@ -112,7 +114,7 @@ export function registerVerifyCompletion(server: McpServer): void { } if (testCmd) { - const testResult = run(testCmd, { timeout: 120000 }); + const testResult = shell(testCmd, { timeout: 120000 }); const testPassed = /pass/i.test(testResult) && !/fail/i.test(testResult); checks.push({ name: "Tests", @@ -130,7 +132,7 @@ export function registerVerifyCompletion(server: McpServer): void { // 4. Build check (only if build script exists and not skipped) if (!skip_build && hasBuildScript()) { - const buildCheck = run(`${pm === "npx" ? "npm run" : pm} build 2>&1 | tail -10`, { timeout: 60000 }); + const buildCheck = shell(`${pm === "npx" ? "npm run" : pm} build 2>&1 | tail -10`, { timeout: 60000 }); const buildPassed = !/\b[Ee]rror\b/.test(buildCheck) || /Successfully compiled/.test(buildCheck); checks.push({ name: "Build",