fix(jq): support file operands and add e2e

docs-internal/registry-parity-worklist.md

@@ -567,6 +567,18 @@ real e2e tests that prove Linux-parity behavior — not smoke tests.
 ### 12. No tests at all — 9 software + 5 agents
 - **Broken:** zero e2e coverage: `gawk, sed, tar, gzip, jq, yq, diffutils,
   file, vim`; agents `claude, codex, opencode, pi, pi-cli`.
+- **Status:**
+  - **jq — DONE.** Added package-local VM e2e coverage for the staged `jq`
+    command and fixed the jaq-backed CLI wrapper to accept Linux-style file
+    operands instead of only stdin. The suite now proves version output,
+    file-backed array filtering, aggregate JSON construction, slurped NDJSON,
+    and invalid JSON parse errors through the packaged WASM command. Proof:
+    `2026-07-08T13-10-55-0700-item12-jq-toolchain-cmd-build-isolated-target.log`;
+    `2026-07-08T13-12-18-0700-item12-jq-package-build-after-wrapper-fix.log`;
+    `2026-07-08T13-12-51-0700-item12-jq-package-e2e-final.log`;
+    `2026-07-08T13-12-51-0700-item12-jq-check-types-final.log`;
+    `2026-07-08T13-12-51-0700-item12-jq-cargo-fmt-check-final.log`.
+    Rev: `slnmvuqz`.
 - **Objective:** write real e2e tests proving each behaves like its Linux
  counterpart (jq processes real JSON, sed edits streams, tar round-trips archives,
   gzip round-trips, etc.); agents exercise the real ACP

software/jq/native/crates/jq/src/lib.rs

@@ -3,6 +3,7 @@
 //! Wraps jaq-core/jaq-std/jaq-json to provide a standard jq CLI interface.
 
 use std::ffi::OsString;
+use std::fs::File as FsFile;
 use std::io::{self, Read, Write};
 
 use jaq_core::load::{Arena, File, Loader};
@@ -40,6 +41,7 @@ struct JqOptions {
     join_output: bool,
     args: Vec<(String, String)>,
     jsonargs: Vec<(String, Val)>,
+    input_paths: Vec<String>,
 }
 
 fn parse_args(args: &[String]) -> Result<JqOptions, String> {
@@ -54,6 +56,7 @@ fn parse_args(args: &[String]) -> Result<JqOptions, String> {
         join_output: false,
         args: Vec::new(),
         jsonargs: Vec::new(),
+        input_paths: Vec::new(),
     };
 
     let mut filter_set = false;
@@ -63,6 +66,17 @@ fn parse_args(args: &[String]) -> Result<JqOptions, String> {
         let arg = &args[i];
 
         if arg == "--" {
+            let remaining = &args[i + 1..];
+            if !filter_set {
+                let Some(filter) = remaining.first() else {
+                    return Err("no filter provided".to_string());
+                };
+                opts.filter = filter.clone();
+                filter_set = true;
+                opts.input_paths.extend(remaining.iter().skip(1).cloned());
+            } else {
+                opts.input_paths.extend(remaining.iter().cloned());
+            }
             break;
         }
 
@@ -118,7 +132,7 @@ fn parse_args(args: &[String]) -> Result<JqOptions, String> {
             opts.filter = arg.clone();
             filter_set = true;
         } else {
-            return Err(format!("unexpected argument: {}", arg));
+            opts.input_paths.push(arg.clone());
         }
 
         i += 1;
@@ -131,30 +145,60 @@ fn parse_args(args: &[String]) -> Result<JqOptions, String> {
     Ok(opts)
 }
 
+fn read_sources(opts: &JqOptions) -> Result<Vec<String>, String> {
+    if opts.input_paths.is_empty() {
+        let mut stdin_data = String::new();
+        io::stdin()
+            .take((MAX_INPUT_BYTES + 1) as u64)
+            .read_to_string(&mut stdin_data)
+            .map_err(|e| format!("failed to read stdin: {}", e))?;
+        if stdin_data.len() > MAX_INPUT_BYTES {
+            return Err("stdin exceeds size limit".to_string());
+        }
+        return Ok(vec![stdin_data]);
+    }
+
+    let mut total = 0usize;
+    let mut sources = Vec::new();
+    for path in &opts.input_paths {
+        let mut data = String::new();
+        if path == "-" {
+            io::stdin()
+                .take((MAX_INPUT_BYTES.saturating_sub(total) + 1) as u64)
+                .read_to_string(&mut data)
+                .map_err(|e| format!("failed to read stdin: {}", e))?;
+        } else {
+            FsFile::open(path)
+                .map_err(|e| format!("failed to open {}: {}", path, e))?
+                .take((MAX_INPUT_BYTES.saturating_sub(total) + 1) as u64)
+                .read_to_string(&mut data)
+                .map_err(|e| format!("failed to read {}: {}", path, e))?;
+        }
+        total = total
+            .checked_add(data.len())
+            .ok_or_else(|| "input exceeds size limit".to_string())?;
+        if total > MAX_INPUT_BYTES {
+            return Err("input exceeds size limit".to_string());
+        }
+        sources.push(data);
+    }
+    Ok(sources)
+}
+
 fn read_inputs(opts: &JqOptions) -> Result<Vec<Val>, String> {
     if opts.null_input {
         return Ok(vec![Val::from(serde_json::Value::Null)]);
     }
 
-    let mut stdin_data = String::new();
-    io::stdin()
-        .take((MAX_INPUT_BYTES + 1) as u64)
-        .read_to_string(&mut stdin_data)
-        .map_err(|e| format!("failed to read stdin: {}", e))?;
-    if stdin_data.len() > MAX_INPUT_BYTES {
-        return Err("stdin exceeds size limit".to_string());
-    }
+    let sources = read_sources(opts)?;
 
     if opts.raw_input {
+        let raw_data = sources.concat();
         if opts.slurp {
-            let mut arr = Vec::new();
-            for line in stdin_data.lines() {
-                push_input_value(&mut arr, serde_json::Value::String(line.to_string()))?;
-            }
-            Ok(vec![Val::from(serde_json::Value::Array(arr))])
+            Ok(vec![Val::from(serde_json::Value::String(raw_data))])
         } else {
             let mut lines = Vec::new();
-            for line in stdin_data.lines() {
+            for line in raw_data.lines() {
                 push_input_value(
                     &mut lines,
                     Val::from(serde_json::Value::String(line.to_string())),
@@ -163,16 +207,23 @@ fn read_inputs(opts: &JqOptions) -> Result<Vec<Val>, String> {
             Ok(lines)
         }
     } else {
-        let trimmed = stdin_data.trim();
-        if trimmed.is_empty() {
-            return Ok(vec![Val::from(serde_json::Value::Null)]);
+        let mut values = Vec::new();
+        for source in &sources {
+            let trimmed = source.trim();
+            if trimmed.is_empty() {
+                continue;
+            }
+
+            let decoder =
+                serde_json::Deserializer::from_str(trimmed).into_iter::<serde_json::Value>();
+            for result in decoder {
+                let value = result.map_err(|e| format!("parse error: {}", e))?;
+                push_input_value(&mut values, value)?;
+            }
         }
 
-        let mut values = Vec::new();
-        let decoder = serde_json::Deserializer::from_str(trimmed).into_iter::<serde_json::Value>();
-        for result in decoder {
-            let value = result.map_err(|e| format!("invalid JSON input: {}", e))?;
-            push_input_value(&mut values, value)?;
+        if values.is_empty() && opts.input_paths.is_empty() {
+            values.push(serde_json::Value::Null);
         }
 
         if opts.slurp {
@@ -217,6 +268,11 @@ fn format_output(val: &Val, opts: &JqOptions) -> Result<String, String> {
 }
 
 fn run_jq(args: &[String]) -> Result<i32, String> {
+    if matches!(args, [arg] if arg == "--version" || arg == "-V") {
+        println!("jq-jaq-{}", env!("CARGO_PKG_VERSION"));
+        return Ok(0);
+    }
+
     let opts = parse_args(args)?;
     let inputs = read_inputs(&opts)?;
 

software/jq/test/jq.test.ts

@@ -0,0 +1,153 @@
+import { existsSync } from "node:fs";
+import { mkdir, mkdtemp, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { dirname, join } from "node:path";
+import { fileURLToPath } from "node:url";
+import {
+	NodeFileSystem,
+	createKernel,
+	createWasmVmRuntime,
+	describeIf,
+} from "@agentos/test-harness";
+import type { Kernel } from "@agentos/test-harness";
+import { afterEach, expect, it } from "vitest";
+
+const JQ_COMMAND_DIR = fileURLToPath(new URL("../bin", import.meta.url));
+const hasJqPackageBinary = existsSync(join(JQ_COMMAND_DIR, "jq"));
+
+let tempRoot: string | undefined;
+
+async function writeFixture(path: string, contents: string): Promise<void> {
+	if (!tempRoot) throw new Error("fixture root not initialized");
+	const hostPath = join(tempRoot, path.replace(/^\/+/, ""));
+	await mkdir(dirname(hostPath), { recursive: true });
+	await writeFile(hostPath, contents);
+}
+
+async function createTestVFS(): Promise<NodeFileSystem> {
+	tempRoot = await mkdtemp(join(tmpdir(), "agentos-jq-"));
+	await writeFixture(
+		"/project/users.json",
+		`${JSON.stringify(
+			{
+				users: [
+					{ name: "Ada", active: true, team: "runtime", score: 7 },
+					{ name: "Grace", active: false, team: "docs", score: 5 },
+					{ name: "Linus", active: true, team: "runtime", score: 3 },
+				],
+			},
+			null,
+			2,
+		)}\n`,
+	);
+	await writeFixture(
+		"/project/events.ndjson",
+		[
+			JSON.stringify({ type: "build", value: 4 }),
+			JSON.stringify({ type: "test", value: 6 }),
+			JSON.stringify({ type: "deploy", value: 2 }),
+		].join("\n") + "\n",
+	);
+	await writeFixture("/project/broken.json", '{"users": [');
+	return new NodeFileSystem({ root: tempRoot });
+}
+
+function lines(stdout: string): string[] {
+	return stdout.split("\n").filter((line) => line.length > 0);
+}
+
+describeIf(hasJqPackageBinary, "jq command", { timeout: 10_000 }, () => {
+	let kernel: Kernel | undefined;
+
+	afterEach(async () => {
+		await kernel?.dispose();
+		kernel = undefined;
+		if (tempRoot) {
+			await rm(tempRoot, { recursive: true, force: true });
+			tempRoot = undefined;
+		}
+	});
+
+	async function mountFixture(): Promise<void> {
+		const vfs = await createTestVFS();
+		kernel = createKernel({ filesystem: vfs });
+		await kernel.mount(createWasmVmRuntime({ commandDirs: [JQ_COMMAND_DIR] }));
+	}
+
+	async function runJq(args: string[]) {
+		if (!kernel) throw new Error("kernel not mounted");
+		let stdout = "";
+		let stderr = "";
+		const proc = kernel.spawn("jq", args, {
+			onStdout: (chunk) => {
+				stdout += Buffer.from(chunk).toString("utf8");
+			},
+			onStderr: (chunk) => {
+				stderr += Buffer.from(chunk).toString("utf8");
+			},
+		});
+		const exitCode = await proc.wait();
+		await new Promise<void>((resolve) => setTimeout(resolve, 0));
+		return { stdout, stderr, exitCode };
+	}
+
+	it("reports a jq-compatible version", async () => {
+		await mountFixture();
+
+		const result = await runJq(["--version"]);
+		expect(result.exitCode, result.stderr || result.stdout).toBe(0);
+		expect(result.stdout).toMatch(/^jq-/);
+	});
+
+	it("filters arrays and emits raw strings", async () => {
+		await mountFixture();
+
+		const result = await runJq([
+			"-r",
+			'.users[] | select(.active) | "\\(.name):\\(.score)"',
+			"/project/users.json",
+		]);
+		expect(result.exitCode, result.stderr || result.stdout).toBe(0);
+		expect(lines(result.stdout)).toEqual(["Ada:7", "Linus:3"]);
+	});
+
+	it("builds aggregate JSON objects", async () => {
+		await mountFixture();
+
+		const result = await runJq([
+			"-c",
+			'{activeNames: [.users[] | select(.active) | .name], runtimeTotal: ([.users[] | select(.team == "runtime") | .score] | add)}',
+			"/project/users.json",
+		]);
+		expect(result.exitCode, result.stderr || result.stdout).toBe(0);
+		expect(JSON.parse(result.stdout.trim())).toEqual({
+			activeNames: ["Ada", "Linus"],
+			runtimeTotal: 10,
+		});
+	});
+
+	it("slurps newline-delimited JSON records", async () => {
+		await mountFixture();
+
+		const result = await runJq([
+			"-s",
+			"-c",
+			"{count: length, total: (map(.value) | add), types: map(.type)}",
+			"/project/events.ndjson",
+		]);
+		expect(result.exitCode, result.stderr || result.stdout).toBe(0);
+		expect(JSON.parse(result.stdout.trim())).toEqual({
+			count: 3,
+			total: 12,
+			types: ["build", "test", "deploy"],
+		});
+	});
+
+	it("fails with a parse error for invalid JSON", async () => {
+		await mountFixture();
+
+		const result = await runJq([".", "/project/broken.json"]);
+		expect(result.exitCode).not.toBe(0);
+		expect(result.stderr).toContain("parse error");
+	});
+});