gsd-pi 2.8.1 → 2.8.2

package/packages/pi-coding-agent/dist/utils/shell.d.ts

@@ -9,6 +9,13 @@ export declare function getShellConfig(): {
     shell: string;
     args: string[];
 };
+/**
+ * On Windows + Git Bash, rewrite Windows-style NUL redirects to /dev/null.
+ * Git Bash doesn't recognize NUL as a device name and creates a literal file
+ * that is undeletable due to NUL being a reserved Windows device name.
+ * No-op on non-Windows platforms.
+ */
+export declare function sanitizeCommand(command: string): string;
 export declare function getShellEnv(): NodeJS.ProcessEnv;
 /**
  * Sanitize binary output for display/storage.

package/packages/pi-coding-agent/dist/utils/shell.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"shell.d.ts","sourceRoot":"","sources":["../../src/utils/shell.ts"],"names":[],"mappings":"AA2CA;;;;;;GAMG;AACH,wBAAgB,cAAc,IAAI;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,EAAE,CAAA;CAAE,CAoElE;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAGvD;AAED,wBAAgB,WAAW,IAAI,MAAM,CAAC,UAAU,CAY/C;AAED;;;;;;;GAOG;AACH,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CA8BxD;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAwBjD"}

package/packages/pi-coding-agent/dist/utils/shell.js

@@ -102,6 +102,17 @@ export function getShellConfig() {
     cachedShellConfig = { shell: "sh", args: ["-c"] };
     return cachedShellConfig;
 }
+/**
+ * On Windows + Git Bash, rewrite Windows-style NUL redirects to /dev/null.
+ * Git Bash doesn't recognize NUL as a device name and creates a literal file
+ * that is undeletable due to NUL being a reserved Windows device name.
+ * No-op on non-Windows platforms.
+ */
+export function sanitizeCommand(command) {
+    if (process.platform !== "win32")
+        return command;
+    return command.replace(/(\d*>>?) *\bNUL\b(?=\s|;|\||&|\)|$)/gi, "$1 /dev/null");
+}
 export function getShellEnv() {
     const binDir = getBinDir();
     const pathKey = Object.keys(process.env).find((key) => key.toLowerCase() === "path") ?? "PATH";

package/packages/pi-coding-agent/dist/utils/shell.js.map

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and trust its output (handles Termux and special filesystems)\n\ttry {\n\t\tconst result = spawnSync(\"which\", [\"bash\"], { encoding: \"utf-8\", timeout: 5000 });\n\t\tif (result.status === 0 && result.stdout) {\n\t\t\tconst firstMatch = result.stdout.trim().split(/\\r?\\n/)[0];\n\t\t\tif (firstMatch) {\n\t\t\t\treturn firstMatch;\n\t\t\t}\n\t\t}\n\t} catch {\n\t\t// Ignore errors\n\t}\n\treturn null;\n}\n\n/**\n * Get shell configuration based on platform.\n * Resolution order:\n * 1. User-specified shellPath in settings.json\n * 2. On Windows: Git Bash in known locations, then bash on PATH\n * 3. On Unix: /bin/bash, then bash on PATH, then fallback to sh\n */\nexport function getShellConfig(): { shell: string; args: string[] } {\n\tif (cachedShellConfig) {\n\t\treturn cachedShellConfig;\n\t}\n\n\tconst settings = SettingsManager.create();\n\tconst customShellPath = settings.getShellPath();\n\n\t// 1. Check user-specified shell path\n\tif (customShellPath) {\n\t\tif (existsSync(customShellPath)) {\n\t\t\tcachedShellConfig = { shell: customShellPath, args: [\"-c\"] };\n\t\t\treturn cachedShellConfig;\n\t\t}\n\t\tthrow new Error(\n\t\t\t`Custom shell path not found: ${customShellPath}\\nPlease update shellPath in ${getSettingsPath()}`,\n\t\t);\n\t}\n\n\tif (process.platform === \"win32\") {\n\t\t// 2. Try Git Bash in known locations\n\t\tconst paths: string[] = [];\n\t\tconst programFiles = process.env.ProgramFiles;\n\t\tif (programFiles) {\n\t\t\tpaths.push(`${programFiles}\\\\Git\\\\bin\\\\bash.exe`);\n\t\t}\n\t\tconst programFilesX86 = process.env[\"ProgramFiles(x86)\"];\n\t\tif (programFilesX86) {\n\t\t\tpaths.push(`${programFilesX86}\\\\Git\\\\bin\\\\bash.exe`);\n\t\t}\n\n\t\tfor (const path of paths) {\n\t\t\tif (existsSync(path)) {\n\t\t\t\tcachedShellConfig = { shell: path, args: [\"-c\"] };\n\t\t\t\treturn cachedShellConfig;\n\t\t\t}\n\t\t}\n\n\t\t// 3. Fallback: search bash.exe on PATH (Cygwin, MSYS2, WSL, etc.)\n\t\tconst bashOnPath = findBashOnPath();\n\t\tif (bashOnPath) {\n\t\t\tcachedShellConfig = { shell: bashOnPath, args: [\"-c\"] };\n\t\t\treturn cachedShellConfig;\n\t\t}\n\n\t\tthrow new Error(\n\t\t\t`No bash shell found. Options:\\n` +\n\t\t\t\t`  1. Install Git for Windows: https://git-scm.com/download/win\\n` +\n\t\t\t\t`  2. Add your bash to PATH (Cygwin, MSYS2, etc.)\\n` +\n\t\t\t\t`  3. Set shellPath in ${getSettingsPath()}\\n\\n` +\n\t\t\t\t`Searched Git Bash in:\\n${paths.map((p) => `  ${p}`).join(\"\\n\")}`,\n\t\t);\n\t}\n\n\t// Unix: try /bin/bash, then bash on PATH, then fallback to sh\n\tif (existsSync(\"/bin/bash\")) {\n\t\tcachedShellConfig = { shell: \"/bin/bash\", args: [\"-c\"] };\n\t\treturn cachedShellConfig;\n\t}\n\n\tconst bashOnPath = findBashOnPath();\n\tif (bashOnPath) {\n\t\tcachedShellConfig = { shell: bashOnPath, args: [\"-c\"] };\n\t\treturn cachedShellConfig;\n\t}\n\n\tcachedShellConfig = { shell: \"sh\", args: [\"-c\"] };\n\treturn cachedShellConfig;\n}\n\nexport function getShellEnv(): NodeJS.ProcessEnv {\n\tconst binDir = getBinDir();\n\tconst pathKey = Object.keys(process.env).find((key) => key.toLowerCase() === \"path\") ?? \"PATH\";\n\tconst currentPath = process.env[pathKey] ?? \"\";\n\tconst pathEntries = currentPath.split(delimiter).filter(Boolean);\n\tconst hasBinDir = pathEntries.includes(binDir);\n\tconst updatedPath = hasBinDir ? currentPath : [binDir, currentPath].filter(Boolean).join(delimiter);\n\n\treturn {\n\t\t...process.env,\n\t\t[pathKey]: updatedPath,\n\t};\n}\n\n/**\n * Sanitize binary output for display/storage.\n * Removes characters that crash string-width or cause display issues:\n * - Control characters (except tab, newline, carriage return)\n * - Lone surrogates\n * - Unicode Format characters (crash string-width due to a bug)\n * - Characters with undefined code points\n */\nexport function sanitizeBinaryOutput(str: string): string {\n\t// Use Array.from to properly iterate over code points (not code units)\n\t// This handles surrogate pairs correctly and catches edge cases where\n\t// codePointAt() might return undefined\n\treturn Array.from(str)\n\t\t.filter((char) => {\n\t\t\t// Filter out characters that cause string-width to crash\n\t\t\t// This includes:\n\t\t\t// - Unicode format characters\n\t\t\t// - Lone surrogates (already filtered by Array.from)\n\t\t\t// - Control chars except \\t \\n \\r\n\t\t\t// - Characters with undefined code points\n\n\t\t\tconst code = char.codePointAt(0);\n\n\t\t\t// Skip if code point is undefined (edge case with invalid strings)\n\t\t\tif (code === undefined) return false;\n\n\t\t\t// Allow tab, newline, carriage return\n\t\t\tif (code === 0x09 || code === 0x0a || code === 0x0d) return true;\n\n\t\t\t// Filter out control characters (0x00-0x1F, except 0x09, 0x0a, 0x0x0d)\n\t\t\tif (code <= 0x1f) return false;\n\n\t\t\t// Filter out Unicode format characters\n\t\t\tif (code >= 0xfff9 && code <= 0xfffb) return false;\n\n\t\t\treturn true;\n\t\t})\n\t\t.join(\"\");\n}\n\n/**\n * Kill a process and all its children (cross-platform)\n */\nexport function killProcessTree(pid: number): void {\n\tif (process.platform === \"win32\") {\n\t\t// Use taskkill on Windows to kill process tree\n\t\ttry {\n\t\t\tspawn(\"taskkill\", [\"/F\", \"/T\", \"/PID\", String(pid)], {\n\t\t\t\tstdio: \"ignore\",\n\t\t\t\tdetached: true,\n\t\t\t});\n\t\t} catch {\n\t\t\t// Ignore errors if taskkill fails\n\t\t}\n\t} else {\n\t\t// Use SIGKILL on Unix/Linux/Mac\n\t\ttry {\n\t\t\tprocess.kill(-pid, \"SIGKILL\");\n\t\t} catch {\n\t\t\t// Fallback to killing just the child if process group kill fails\n\t\t\ttry {\n\t\t\t\tprocess.kill(pid, \"SIGKILL\");\n\t\t\t} catch {\n\t\t\t\t// Process already dead\n\t\t\t}\n\t\t}\n\t}\n}\n"]}
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{ existsSync } from \"node:fs\";\nimport { delimiter } from \"node:path\";\nimport { spawn, spawnSync } from \"child_process\";\nimport { getBinDir, getSettingsPath } from \"../config.js\";\nimport { SettingsManager } from \"../core/settings-manager.js\";\n\nlet cachedShellConfig: { shell: string; args: string[] } | null = null;\n\n/**\n * Find bash executable on PATH (cross-platform)\n */\nfunction findBashOnPath(): string | null {\n\tif (process.platform === \"win32\") {\n\t\t// Windows: Use 'where' and verify file exists (where can return non-existent paths)\n\t\ttry {\n\t\t\tconst result = spawnSync(\"where\", [\"bash.exe\"], { encoding: \"utf-8\", timeout: 5000 });\n\t\t\tif (result.status === 0 && result.stdout) {\n\t\t\t\tconst firstMatch = result.stdout.trim().split(/\\r?\\n/)[0];\n\t\t\t\tif (firstMatch && existsSync(firstMatch)) {\n\t\t\t\t\treturn firstMatch;\n\t\t\t\t}\n\t\t\t}\n\t\t} catch {\n\t\t\t// Ignore errors\n\t\t}\n\t\treturn null;\n\t}\n\n\t// Unix: Use 'which' and trust its output (handles Termux and special filesystems)\n\ttry {\n\t\tconst result = spawnSync(\"which\", [\"bash\"], { encoding: \"utf-8\", timeout: 5000 });\n\t\tif (result.status === 0 && result.stdout) {\n\t\t\tconst firstMatch = result.stdout.trim().split(/\\r?\\n/)[0];\n\t\t\tif (firstMatch) {\n\t\t\t\treturn firstMatch;\n\t\t\t}\n\t\t}\n\t} catch {\n\t\t// Ignore errors\n\t}\n\treturn null;\n}\n\n/**\n * Get shell configuration based on platform.\n * Resolution order:\n * 1. User-specified shellPath in settings.json\n * 2. On Windows: Git Bash in known locations, then bash on PATH\n * 3. On Unix: /bin/bash, then bash on PATH, then fallback to sh\n */\nexport function getShellConfig(): { shell: string; args: string[] } {\n\tif (cachedShellConfig) {\n\t\treturn cachedShellConfig;\n\t}\n\n\tconst settings = SettingsManager.create();\n\tconst customShellPath = settings.getShellPath();\n\n\t// 1. Check user-specified shell path\n\tif (customShellPath) {\n\t\tif (existsSync(customShellPath)) {\n\t\t\tcachedShellConfig = { shell: customShellPath, args: [\"-c\"] };\n\t\t\treturn cachedShellConfig;\n\t\t}\n\t\tthrow new Error(\n\t\t\t`Custom shell path not found: ${customShellPath}\\nPlease update shellPath in ${getSettingsPath()}`,\n\t\t);\n\t}\n\n\tif (process.platform === \"win32\") {\n\t\t// 2. Try Git Bash in known locations\n\t\tconst paths: string[] = [];\n\t\tconst programFiles = process.env.ProgramFiles;\n\t\tif (programFiles) {\n\t\t\tpaths.push(`${programFiles}\\\\Git\\\\bin\\\\bash.exe`);\n\t\t}\n\t\tconst programFilesX86 = process.env[\"ProgramFiles(x86)\"];\n\t\tif (programFilesX86) {\n\t\t\tpaths.push(`${programFilesX86}\\\\Git\\\\bin\\\\bash.exe`);\n\t\t}\n\n\t\tfor (const path of paths) {\n\t\t\tif (existsSync(path)) {\n\t\t\t\tcachedShellConfig = { shell: path, args: [\"-c\"] };\n\t\t\t\treturn cachedShellConfig;\n\t\t\t}\n\t\t}\n\n\t\t// 3. Fallback: search bash.exe on PATH (Cygwin, MSYS2, WSL, etc.)\n\t\tconst bashOnPath = findBashOnPath();\n\t\tif (bashOnPath) {\n\t\t\tcachedShellConfig = { shell: bashOnPath, args: [\"-c\"] };\n\t\t\treturn cachedShellConfig;\n\t\t}\n\n\t\tthrow new Error(\n\t\t\t`No bash shell found. Options:\\n` +\n\t\t\t\t`  1. Install Git for Windows: https://git-scm.com/download/win\\n` +\n\t\t\t\t`  2. Add your bash to PATH (Cygwin, MSYS2, etc.)\\n` +\n\t\t\t\t`  3. Set shellPath in ${getSettingsPath()}\\n\\n` +\n\t\t\t\t`Searched Git Bash in:\\n${paths.map((p) => `  ${p}`).join(\"\\n\")}`,\n\t\t);\n\t}\n\n\t// Unix: try /bin/bash, then bash on PATH, then fallback to sh\n\tif (existsSync(\"/bin/bash\")) {\n\t\tcachedShellConfig = { shell: \"/bin/bash\", args: [\"-c\"] };\n\t\treturn cachedShellConfig;\n\t}\n\n\tconst bashOnPath = findBashOnPath();\n\tif (bashOnPath) {\n\t\tcachedShellConfig = { shell: bashOnPath, args: [\"-c\"] };\n\t\treturn cachedShellConfig;\n\t}\n\n\tcachedShellConfig = { shell: \"sh\", args: [\"-c\"] };\n\treturn cachedShellConfig;\n}\n\n/**\n * On Windows + Git Bash, rewrite Windows-style NUL redirects to /dev/null.\n * Git Bash doesn't recognize NUL as a device name and creates a literal file\n * that is undeletable due to NUL being a reserved Windows device name.\n * No-op on non-Windows platforms.\n */\nexport function sanitizeCommand(command: string): string {\n\tif (process.platform !== \"win32\") return command;\n\treturn command.replace(/(\\d*>>?) *\\bNUL\\b(?=\\s|;|\\||&|\\)|$)/gi, \"$1 /dev/null\");\n}\n\nexport function getShellEnv(): NodeJS.ProcessEnv {\n\tconst binDir = getBinDir();\n\tconst pathKey = Object.keys(process.env).find((key) => key.toLowerCase() === \"path\") ?? \"PATH\";\n\tconst currentPath = process.env[pathKey] ?? \"\";\n\tconst pathEntries = currentPath.split(delimiter).filter(Boolean);\n\tconst hasBinDir = pathEntries.includes(binDir);\n\tconst updatedPath = hasBinDir ? currentPath : [binDir, currentPath].filter(Boolean).join(delimiter);\n\n\treturn {\n\t\t...process.env,\n\t\t[pathKey]: updatedPath,\n\t};\n}\n\n/**\n * Sanitize binary output for display/storage.\n * Removes characters that crash string-width or cause display issues:\n * - Control characters (except tab, newline, carriage return)\n * - Lone surrogates\n * - Unicode Format characters (crash string-width due to a bug)\n * - Characters with undefined code points\n */\nexport function sanitizeBinaryOutput(str: string): string {\n\t// Use Array.from to properly iterate over code points (not code units)\n\t// This handles surrogate pairs correctly and catches edge cases where\n\t// codePointAt() might return undefined\n\treturn Array.from(str)\n\t\t.filter((char) => {\n\t\t\t// Filter out characters that cause string-width to crash\n\t\t\t// This includes:\n\t\t\t// - Unicode format characters\n\t\t\t// - Lone surrogates (already filtered by Array.from)\n\t\t\t// - Control chars except \\t \\n \\r\n\t\t\t// - Characters with undefined code points\n\n\t\t\tconst code = char.codePointAt(0);\n\n\t\t\t// Skip if code point is undefined (edge case with invalid strings)\n\t\t\tif (code === undefined) return false;\n\n\t\t\t// Allow tab, newline, carriage return\n\t\t\tif (code === 0x09 || code === 0x0a || code === 0x0d) return true;\n\n\t\t\t// Filter out control characters (0x00-0x1F, except 0x09, 0x0a, 0x0x0d)\n\t\t\tif (code <= 0x1f) return false;\n\n\t\t\t// Filter out Unicode format characters\n\t\t\tif (code >= 0xfff9 && code <= 0xfffb) return false;\n\n\t\t\treturn true;\n\t\t})\n\t\t.join(\"\");\n}\n\n/**\n * Kill a process and all its children (cross-platform)\n */\nexport function killProcessTree(pid: number): void {\n\tif (process.platform === \"win32\") {\n\t\t// Use taskkill on Windows to kill process tree\n\t\ttry {\n\t\t\tspawn(\"taskkill\", [\"/F\", \"/T\", \"/PID\", String(pid)], {\n\t\t\t\tstdio: \"ignore\",\n\t\t\t\tdetached: true,\n\t\t\t});\n\t\t} catch {\n\t\t\t// Ignore errors if taskkill fails\n\t\t}\n\t} else {\n\t\t// Use SIGKILL on Unix/Linux/Mac\n\t\ttry {\n\t\t\tprocess.kill(-pid, \"SIGKILL\");\n\t\t} catch {\n\t\t\t// Fallback to killing just the child if process group kill fails\n\t\t\ttry {\n\t\t\t\tprocess.kill(pid, \"SIGKILL\");\n\t\t\t} catch {\n\t\t\t\t// Process already dead\n\t\t\t}\n\t\t}\n\t}\n}\n"]}

package/packages/pi-coding-agent/src/core/bash-executor.ts

@@ -12,7 +12,7 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { type ChildProcess, spawn } from "child_process";
 import stripAnsi from "strip-ansi";
-import { getShellConfig, getShellEnv, killProcessTree, sanitizeBinaryOutput } from "../utils/shell.js";
+import { getShellConfig, getShellEnv, killProcessTree, sanitizeBinaryOutput, sanitizeCommand } from "../utils/shell.js";
 import type { BashOperations } from "./tools/bash.js";
 import { DEFAULT_MAX_BYTES, truncateTail } from "./tools/truncate.js";
 
@@ -61,7 +61,7 @@ export interface BashResult {
 export function executeBash(command: string, options?: BashExecutorOptions): Promise<BashResult> {
 	return new Promise((resolve, reject) => {
 		const { shell, args } = getShellConfig();
-		const child: ChildProcess = spawn(shell, [...args, command], {
+		const child: ChildProcess = spawn(shell, [...args, sanitizeCommand(command)], {
 			detached: true,
 			env: getShellEnv(),
 			stdio: ["ignore", "pipe", "pipe"],

package/packages/pi-coding-agent/src/core/tools/bash.ts

@@ -6,7 +6,7 @@ import { join } from "node:path";
 import type { AgentTool } from "@gsd/pi-agent-core";
 import { type Static, Type } from "@sinclair/typebox";
 import { spawn } from "child_process";
-import { getShellConfig, getShellEnv, killProcessTree } from "../../utils/shell.js";
+import { getShellConfig, getShellEnv, killProcessTree, sanitizeCommand } from "../../utils/shell.js";
 import { DEFAULT_MAX_BYTES, DEFAULT_MAX_LINES, formatSize, type TruncationResult, truncateTail } from "./truncate.js";
 import type { ArtifactManager } from "../artifact-manager.js";
 
@@ -211,7 +211,7 @@ export function createBashTool(cwd: string, options?: BashToolOptions): AgentToo
 			onUpdate?,
 		) => {
 			// Apply command prefix if configured (e.g., "shopt -s expand_aliases" for alias support)
-			const resolvedCommand = commandPrefix ? `${commandPrefix}\n${command}` : command;
+			const resolvedCommand = sanitizeCommand(commandPrefix ? `${commandPrefix}\n${command}` : command);
 			const spawnContext = resolveSpawnContext(resolvedCommand, cwd, spawnHook);
 
 			return new Promise((resolve, reject) => {

package/packages/pi-coding-agent/src/core/tools/path-utils.test.ts

@@ -0,0 +1,66 @@
+import { describe, it, mock, afterEach } from "node:test";
+import assert from "node:assert/strict";
+import { resolveToCwd, expandPath } from "./path-utils.js";
+
+describe("resolveToCwd", () => {
+	it("resolves relative paths against cwd", () => {
+		const result = resolveToCwd("foo/bar.txt", "/home/user/project");
+		assert.equal(result, "/home/user/project/foo/bar.txt");
+	});
+
+	it("returns absolute paths unchanged", () => {
+		const result = resolveToCwd("/absolute/path.txt", "/home/user/project");
+		assert.equal(result, "/absolute/path.txt");
+	});
+
+	it("expands ~ to home directory", () => {
+		const result = resolveToCwd("~/file.txt", "/home/user/project");
+		assert.ok(result.endsWith("/file.txt"));
+		assert.ok(!result.includes("~"));
+	});
+});
+
+describe("normalizeMsysPath (via resolveToCwd on win32)", () => {
+	const originalPlatform = process.platform;
+
+	afterEach(() => {
+		Object.defineProperty(process, "platform", { value: originalPlatform });
+	});
+
+	it("converts /c/Users/... to C:\\Users\\... on win32", () => {
+		Object.defineProperty(process, "platform", { value: "win32" });
+		// Re-import to pick up platform change — but since normalizeMsysPath
+		// reads process.platform at call time, we can test directly.
+		// On non-Windows, resolveToCwd treats /c/Users as absolute, so we
+		// test the normalization logic by checking the MSYS regex behavior.
+		const msysPath = "/c/Users/test/project";
+		const msysRegex = /^\/[a-zA-Z]\//;
+		assert.ok(msysRegex.test(msysPath), "MSYS path pattern matches");
+
+		// Simulate the conversion
+		const converted = `${msysPath[1].toUpperCase()}:\\${msysPath.slice(3).replace(/\//g, "\\")}`;
+		assert.equal(converted, "C:\\Users\\test\\project");
+	});
+
+	it("converts /f/Projects to F:\\Projects on win32", () => {
+		const msysPath = "/f/Projects";
+		const converted = `${msysPath[1].toUpperCase()}:\\${msysPath.slice(3).replace(/\//g, "\\")}`;
+		assert.equal(converted, "F:\\Projects");
+	});
+
+	it("does not convert regular Unix paths", () => {
+		const regularPath = "/usr/local/bin";
+		const msysRegex = /^\/[a-zA-Z]\//;
+		// /u/local/bin would match, but /usr/local/bin has 3+ chars before /
+		// Actually /u/ would match — but /usr/ won't because 'us' is 2 chars.
+		// The regex checks single letter after leading slash.
+		assert.ok(!msysRegex.test("/usr/local/bin"), "/usr/... is not an MSYS path");
+		assert.ok(msysRegex.test("/u/local/bin"), "/u/... would match (single letter)");
+	});
+
+	it("does not convert paths without leading slash", () => {
+		const msysRegex = /^\/[a-zA-Z]\//;
+		assert.ok(!msysRegex.test("c/Users/test"), "no leading slash — not MSYS");
+		assert.ok(!msysRegex.test("relative/path"), "relative path — not MSYS");
+	});
+});

package/packages/pi-coding-agent/src/core/tools/path-utils.ts

@@ -47,12 +47,24 @@ export function expandPath(filePath: string): string {
 	return normalized;
 }
 
+/**
+ * On Windows, convert MSYS/MinGW-style paths (/c/Users/...) to native
+ * drive letter paths (C:\Users\...). LLMs often produce these when given
+ * Windows paths in prompts.
+ */
+function normalizeMsysPath(p: string): string {
+	if (process.platform === "win32" && /^\/[a-zA-Z]\//.test(p)) {
+		return `${p[1]!.toUpperCase()}:\\${p.slice(3).replace(/\//g, "\\")}`;
+	}
+	return p;
+}
+
 /**
  * Resolve a path relative to the given cwd.
- * Handles ~ expansion and absolute paths.
+ * Handles ~ expansion, MSYS-style paths on Windows, and absolute paths.
  */
 export function resolveToCwd(filePath: string, cwd: string): string {
-	const expanded = expandPath(filePath);
+	const expanded = normalizeMsysPath(expandPath(filePath));
 	if (isAbsolute(expanded)) {
 		return expanded;
 	}

package/packages/pi-coding-agent/src/index.ts

@@ -333,4 +333,4 @@ export {
 export { copyToClipboard } from "./utils/clipboard.js";
 export { parseFrontmatter, stripFrontmatter } from "./utils/frontmatter.js";
 // Shell utilities
-export { getShellConfig } from "./utils/shell.js";
+export { getShellConfig, sanitizeCommand } from "./utils/shell.js";

package/packages/pi-coding-agent/src/modes/interactive/interactive-mode.ts

@@ -824,10 +824,12 @@ export class InteractiveMode {
 
 		// Try parent directories (package manager stores directory paths)
 		let current = p;
-		while (current.includes("/")) {
-			current = current.substring(0, current.lastIndexOf("/"));
-			const parent = metadata.get(current);
-			if (parent) return parent;
+		let parent = path.dirname(current);
+		while (parent !== current) {
+			const meta = metadata.get(parent);
+			if (meta) return meta;
+			current = parent;
+			parent = path.dirname(current);
 		}
 
 		return undefined;

package/packages/pi-coding-agent/src/utils/shell.ts

@@ -118,6 +118,17 @@ export function getShellConfig(): { shell: string; args: string[] } {
 	return cachedShellConfig;
 }
 
+/**
+ * On Windows + Git Bash, rewrite Windows-style NUL redirects to /dev/null.
+ * Git Bash doesn't recognize NUL as a device name and creates a literal file
+ * that is undeletable due to NUL being a reserved Windows device name.
+ * No-op on non-Windows platforms.
+ */
+export function sanitizeCommand(command: string): string {
+	if (process.platform !== "win32") return command;
+	return command.replace(/(\d*>>?) *\bNUL\b(?=\s|;|\||&|\)|$)/gi, "$1 /dev/null");
+}
+
 export function getShellEnv(): NodeJS.ProcessEnv {
 	const binDir = getBinDir();
 	const pathKey = Object.keys(process.env).find((key) => key.toLowerCase() === "path") ?? "PATH";

package/src/resources/extensions/bg-shell/index.ts

@@ -34,6 +34,7 @@ import {
 	DEFAULT_MAX_BYTES,
 	DEFAULT_MAX_LINES,
 	getShellConfig,
+	sanitizeCommand,
 } from "@gsd/pi-coding-agent";
 import {
 	Text,
@@ -582,7 +583,7 @@ function startProcess(opts: StartOptions): BgProcess {
 	const env = { ...process.env, ...(opts.env || {}) };
 
 	const { shell, args: shellArgs } = getShellConfig();
-	const proc = spawn(shell, [...shellArgs, opts.command], {
+	const proc = spawn(shell, [...shellArgs, sanitizeCommand(opts.command)], {
 		cwd: opts.cwd,
 		stdio: ["pipe", "pipe", "pipe"],
 		env,

package/src/resources/extensions/gsd/auto.ts

@@ -48,14 +48,14 @@ import {
   validateCompleteBoundary,
   formatValidationIssues,
 } from "./observability-validator.js";
-import { ensureGitignore } from "./gitignore.js";
+import { ensureGitignore, untrackRuntimeFiles } from "./gitignore.js";
 import { runGSDDoctor, rebuildState } from "./doctor.js";
 import { snapshotSkills, clearSkillSnapshot } from "./skill-discovery.js";
 import {
   initMetrics, resetMetrics, snapshotUnitMetrics, getLedger,
   getProjectTotals, formatCost, formatTokenCount,
 } from "./metrics.js";
-import { join } from "node:path";
+import { dirname, join } from "node:path";
 import { readdirSync, readFileSync, existsSync, mkdirSync, writeFileSync } from "node:fs";
 import { execSync, execFileSync } from "node:child_process";
 import {
@@ -381,6 +381,7 @@ export async function startAuto(
 
   // Ensure .gitignore has baseline patterns
   ensureGitignore(base);
+  untrackRuntimeFiles(base);
 
   // Bootstrap .gsd/ if it doesn't exist
   const gsdDir = join(base, ".gsd");
@@ -1696,13 +1697,11 @@ async function buildResearchMilestonePrompt(mid: string, midTitle: string, base:
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
   const outputRelPath = relMilestoneFile(base, mid, "RESEARCH");
-  const outputAbsPath = resolveMilestoneFile(base, mid, "RESEARCH") ?? join(base, outputRelPath);
   return loadPrompt("research-milestone", {
     milestoneId: mid, milestoneTitle: midTitle,
     milestonePath: relMilestonePath(base, mid),
     contextPath: contextRel,
     outputPath: outputRelPath,
-    outputAbsPath,
     inlinedContext,
     ...buildSkillDiscoveryVars(),
   });
@@ -1730,7 +1729,6 @@ async function buildPlanMilestonePrompt(mid: string, midTitle: string, base: str
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
   const outputRelPath = relMilestoneFile(base, mid, "ROADMAP");
-  const outputAbsPath = resolveMilestoneFile(base, mid, "ROADMAP") ?? join(base, outputRelPath);
   const secretsOutputPath = relMilestoneFile(base, mid, "SECRETS");
   return loadPrompt("plan-milestone", {
     milestoneId: mid, milestoneTitle: midTitle,
@@ -1738,7 +1736,6 @@ async function buildPlanMilestonePrompt(mid: string, midTitle: string, base: str
     contextPath: contextRel,
     researchPath: researchRel,
     outputPath: outputRelPath,
-    outputAbsPath,
     secretsOutputPath,
     inlinedContext,
   });
@@ -1770,7 +1767,6 @@ async function buildResearchSlicePrompt(
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
   const outputRelPath = relSliceFile(base, mid, sid, "RESEARCH");
-  const outputAbsPath = resolveSliceFile(base, mid, sid, "RESEARCH") ?? join(base, outputRelPath);
   return loadPrompt("research-slice", {
     milestoneId: mid, sliceId: sid, sliceTitle: sTitle,
     slicePath: relSlicePath(base, mid, sid),
@@ -1778,7 +1774,6 @@ async function buildResearchSlicePrompt(
     contextPath: contextRel,
     milestoneResearchPath: milestoneResearchRel,
     outputPath: outputRelPath,
-    outputAbsPath,
     inlinedContext,
     dependencySummaries: depContent,
     ...buildSkillDiscoveryVars(),
@@ -1807,16 +1802,12 @@ async function buildPlanSlicePrompt(
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
   const outputRelPath = relSliceFile(base, mid, sid, "PLAN");
-  const outputAbsPath = resolveSliceFile(base, mid, sid, "PLAN") ?? join(base, outputRelPath);
-  const sliceAbsPath = resolveSlicePath(base, mid, sid) ?? join(base, relSlicePath(base, mid, sid));
   return loadPrompt("plan-slice", {
     milestoneId: mid, sliceId: sid, sliceTitle: sTitle,
     slicePath: relSlicePath(base, mid, sid),
-    sliceAbsPath,
     roadmapPath: roadmapRel,
     researchPath: researchRel,
     outputPath: outputRelPath,
-    outputAbsPath,
     inlinedContext,
     dependencySummaries: depContent,
   });
@@ -1867,8 +1858,7 @@ async function buildExecuteTaskPrompt(
 
   const carryForwardSection = await buildCarryForwardSection(priorSummaries, base);
 
-  const sliceDirAbs = resolveSlicePath(base, mid, sid) ?? join(base, relSlicePath(base, mid, sid));
-  const taskSummaryAbsPath = join(sliceDirAbs, "tasks", `${tid}-SUMMARY.md`);
+  const taskSummaryPath = `${relSlicePath(base, mid, sid)}/tasks/${tid}-SUMMARY.md`;
 
   return loadPrompt("execute-task", {
     milestoneId: mid, sliceId: sid, sliceTitle: sTitle, taskId: tid, taskTitle: tTitle,
@@ -1880,7 +1870,7 @@ async function buildExecuteTaskPrompt(
     carryForwardSection,
     resumeSection,
     priorTaskLines: priorLines,
-    taskSummaryAbsPath,
+    taskSummaryPath,
   });
 }
 
@@ -1916,17 +1906,17 @@ async function buildCompleteSlicePrompt(
 
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
-  const sliceDirAbs = resolveSlicePath(base, mid, sid) ?? join(base, relSlicePath(base, mid, sid));
-  const sliceSummaryAbsPath = join(sliceDirAbs, `${sid}-SUMMARY.md`);
-  const sliceUatAbsPath = join(sliceDirAbs, `${sid}-UAT.md`);
+  const sliceRel = relSlicePath(base, mid, sid);
+  const sliceSummaryPath = `${sliceRel}/${sid}-SUMMARY.md`;
+  const sliceUatPath = `${sliceRel}/${sid}-UAT.md`;
 
   return loadPrompt("complete-slice", {
     milestoneId: mid, sliceId: sid, sliceTitle: sTitle,
-    slicePath: relSlicePath(base, mid, sid),
+    slicePath: sliceRel,
     roadmapPath: roadmapRel,
     inlinedContext,
-    sliceSummaryAbsPath,
-    sliceUatAbsPath,
+    sliceSummaryPath,
+    sliceUatPath,
   });
 }
 
@@ -1965,15 +1955,14 @@ async function buildCompleteMilestonePrompt(
 
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
-  const milestoneDirAbs = resolveMilestonePath(base, mid) ?? join(base, relMilestonePath(base, mid));
-  const milestoneSummaryAbsPath = join(milestoneDirAbs, `${mid}-SUMMARY.md`);
+  const milestoneSummaryPath = `${relMilestonePath(base, mid)}/${mid}-SUMMARY.md`;
 
   return loadPrompt("complete-milestone", {
     milestoneId: mid,
     milestoneTitle: midTitle,
     roadmapPath: roadmapRel,
     inlinedContext,
-    milestoneSummaryAbsPath,
+    milestoneSummaryPath,
   });
 }
 
@@ -2016,8 +2005,7 @@ async function buildReplanSlicePrompt(
 
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
-  const sliceDirAbs = resolveSlicePath(base, mid, sid) ?? join(base, relSlicePath(base, mid, sid));
-  const replanAbsPath = join(sliceDirAbs, `${sid}-REPLAN.md`);
+  const replanPath = `${relSlicePath(base, mid, sid)}/${sid}-REPLAN.md`;
 
   return loadPrompt("replan-slice", {
     milestoneId: mid,
@@ -2027,7 +2015,7 @@ async function buildReplanSlicePrompt(
     planPath: slicePlanRel,
     blockerTaskId,
     inlinedContext,
-    replanAbsPath,
+    replanPath,
   });
 }
 
@@ -2145,8 +2133,6 @@ async function buildRunUatPrompt(
 
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
-  const sliceDirAbs = resolveSlicePath(base, mid, sliceId) ?? join(base, relSlicePath(base, mid, sliceId));
-  const uatResultAbsPath = join(sliceDirAbs, `${sliceId}-UAT-RESULT.md`);
   const uatResultPath = relSliceFile(base, mid, sliceId, "UAT-RESULT");
   const uatType = extractUatType(uatContent) ?? "human-experience";
 
@@ -2154,7 +2140,6 @@ async function buildRunUatPrompt(
     milestoneId: mid,
     sliceId,
     uatPath,
-    uatResultAbsPath,
     uatResultPath,
     uatType,
     inlinedContext,
@@ -2181,9 +2166,7 @@ async function buildReassessRoadmapPrompt(
 
   const inlinedContext = `## Inlined Context (preloaded — do not re-read these files)\n\n${inlined.join("\n\n---\n\n")}`;
 
-  const assessmentRel = relSliceFile(base, mid, completedSliceId, "ASSESSMENT");
-  const sliceDirAbs = resolveSlicePath(base, mid, completedSliceId) ?? join(base, relSlicePath(base, mid, completedSliceId));
-  const assessmentAbsPath = join(sliceDirAbs, `${completedSliceId}-ASSESSMENT.md`);
+  const assessmentPath = relSliceFile(base, mid, completedSliceId, "ASSESSMENT");
 
   return loadPrompt("reassess-roadmap", {
     milestoneId: mid,
@@ -2191,8 +2174,7 @@ async function buildReassessRoadmapPrompt(
     completedSliceId,
     roadmapPath: roadmapRel,
     completedSliceSummaryPath: summaryRel,
-    assessmentPath: assessmentRel,
-    assessmentAbsPath,
+    assessmentPath,
     inlinedContext,
   });
 }
@@ -2814,7 +2796,7 @@ function verifyExpectedArtifact(unitType: string, unitId: string, base: string):
 export function writeBlockerPlaceholder(unitType: string, unitId: string, base: string, reason: string): string | null {
   const absPath = resolveExpectedArtifactPath(unitType, unitId, base);
   if (!absPath) return null;
-  const dir = absPath.substring(0, absPath.lastIndexOf("/"));
+  const dir = dirname(absPath);
   if (!existsSync(dir)) mkdirSync(dir, { recursive: true });
   const content = [
     `# BLOCKER — auto-mode recovery failed`,

package/src/resources/extensions/gsd/docs/preferences-reference.md

@@ -13,6 +13,61 @@ Full documentation for `~/.gsd/preferences.md` (global) and `.gsd/preferences.md
 
 ---
 
+## Semantics
+
+### Empty Arrays vs Omitted Fields
+
+**Empty arrays (`[]`) are equivalent to omitting the field entirely.** During validation, GSD deletes empty arrays from the preferences object (see `validatePreferences()` in `preferences.ts`):
+
+```typescript
+for (const key of ["always_use_skills", "prefer_skills", "avoid_skills", "custom_instructions"] as const) {
+  if (validated[key] && validated[key]!.length === 0) {
+    delete validated[key];
+  }
+}
+```
+
+These are functionally identical:
+
+```yaml
+# Explicit empty arrays — will be normalized away
+prefer_skills: []
+avoid_skills: []
+skill_rules: []
+
+# Omitted entirely — same result
+# (just don't write these fields)
+```
+
+**Recommendation:** Omit fields you don't need. Empty arrays add noise with no effect.
+
+### Global vs Project Preferences
+
+Preferences are loaded from two locations and merged:
+
+1. **Global:** `~/.gsd/preferences.md` — applies to all projects
+2. **Project:** `.gsd/preferences.md` — applies to the current project only
+
+**Merge behavior** (see `mergePreferences()` in `preferences.ts`):
+- **Scalar fields** (`skill_discovery`, `budget_ceiling`, etc.): Project wins if defined, otherwise global. Uses nullish coalescing (`??`).
+- **Array fields** (`always_use_skills`, `prefer_skills`, etc.): Concatenated via `mergeStringLists()` (global first, then project).
+- **Object fields** (`models`, `git`, `auto_supervisor`): Shallow merge via spread operator `{ ...base, ...override }`.
+
+For `models`, project settings override global at the phase level. If global has `planning: opus` and project has `planning: sonnet`, the project wins. But if project omits `research`, global's `research` setting is preserved.
+
+### Skill Discovery vs Skill Preferences
+
+These are **separate concerns**:
+
+| Field | What it controls | Code reference |
+|-------|-----------------|----------------|
+| `skill_discovery` | **Whether** GSD looks for relevant skills during research | `resolveSkillDiscoveryMode()` in `preferences.ts` |
+| `always_use_skills`, `prefer_skills`, `avoid_skills` | **Which** skills to use when they're found relevant | `renderPreferencesForSystemPrompt()` in `preferences.ts` |
+
+Setting `prefer_skills: []` does **not** disable skill discovery — it just means you have no preference overrides. Use `skill_discovery: off` to disable discovery entirely.
+
+---
+
 ## Field Guide
 
 - `version`: schema version. Start at `1`.
@@ -60,6 +115,27 @@ Full documentation for `~/.gsd/preferences.md` (global) and `.gsd/preferences.md
 - Use `skill_rules` for situational routing, not broad personality preferences.
 - Prefer skill names for stable built-in skills.
 - Prefer absolute paths for local personal skills.
+- **Omit fields you don't need** — empty arrays add noise with no effect.
+
+---
+
+## Minimal Example
+
+The cleanest preferences file only specifies what you actually want:
+
+```yaml
+---
+version: 1
+always_use_skills:
+  - debug-like-expert
+skill_discovery: suggest
+models:
+  planning: claude-opus-4-6
+  execution: claude-sonnet-4-6
+---
+```
+
+Everything else uses defaults. No `prefer_skills: []`, no `avoid_skills: []`, no `auto_supervisor: {}` — those are just noise.
 
 ---
 

package/src/resources/extensions/gsd/gitignore.ts

@@ -8,6 +8,7 @@
 
 import { join } from "node:path";
 import { existsSync, readFileSync, writeFileSync } from "node:fs";
+import { execSync } from "node:child_process";
 
 /**
  * Patterns that are always correct regardless of project type.
@@ -106,6 +107,32 @@ export function ensureGitignore(basePath: string): boolean {
   return true;
 }
 
+/**
+ * Remove BASELINE_PATTERNS runtime paths from the git index if they are
+ * currently tracked. This fixes repos that started tracking these files
+ * before the .gitignore rule was added — git continues tracking files
+ * already in the index even after .gitignore is updated.
+ *
+ * Only removes from the index (`--cached`), never from disk. Idempotent.
+ */
+export function untrackRuntimeFiles(basePath: string): void {
+  // The GSD runtime paths are the first 7 entries in BASELINE_PATTERNS
+  const runtimePaths = BASELINE_PATTERNS.slice(0, 7);
+
+  for (const pattern of runtimePaths) {
+    // Use -r for directory patterns (trailing slash), strip the slash for the command
+    const target = pattern.endsWith("/") ? pattern.slice(0, -1) : pattern;
+    try {
+      execSync(`git rm -r --cached ${target}`, {
+        cwd: basePath,
+        stdio: ["ignore", "ignore", "ignore"],
+      });
+    } catch {
+      // File not tracked or doesn't exist — expected, ignore
+    }
+  }
+}
+
 /**
  * Ensure basePath/.gsd/PREFERENCES.md exists as an empty template.
  * Creates the file with frontmatter only if it doesn't exist.