pi-vault-mind 0.16.31 → 0.16.33

package/CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## 0.16.33 — 2026-08-29
+
+### Added
+
+- **Content-writing-system runtime.** `pvm setup` now installs the private `content-writing-system` Pi package (`git:git@github.com:kylebrodeur/content-writing-system`) as a required extension, registering both its skill and the `/check-writing` command in the vault-local agent. Requires git/SSH access to the repository at setup time.
+
+### Changed
+
+- **Idempotent extension install.** `pvm setup` now reads the vault-local `settings.json` and skips extensions already present at the recorded spec (including pinned versions), reinstalling only missing specs or changed version pins. Repeated `pvm setup` / `--resources-only` runs no longer re-clone or re-fetch unchanged extensions.
+
+## 0.16.32 — 2026-08-28
+
+### Changed
+
+- **Concise setup progress.** `pvm setup` now reports one bounded progress line per extension and curated skill while preserving captured installer diagnostics on failure.
+
+### Fixed
+
+- **Vault-isolated main sessions.** `pvm run` disables implicit skill and prompt-template discovery, then explicitly loads only curated and package skills rooted in the vault-local agent directory. Specialist skill availability can no longer select a specialist identity for the interactive main session.
+- **Escaping package paths.** Setup removes local package paths that resolve outside the vault-local agent directory while preserving npm packages and in-runtime custom packages.
+
 ## 0.16.31 — 2026-08-28
 
 ### Added

package/README.md

@@ -123,37 +123,32 @@ obsidian plugin:install id=obsidian42-brat enable
 # In Obsidian: Settings → BRAT → Beta Plugin List → Add
 ```
 
-### Recommended: kepano/obsidian-skills (pi skills)
+### Curated vault-local skills
 
-Install via the official [`skills` CLI](https://github.com/vercel-labs/skills)
-(pi is a first-class target agent — auto-detected):
+`pvm setup` installs the supported Obsidian and NotebookLM skills into the
+vault-local Pi agent directory:
 
 ```bash
-# Non-interactive: install all 5 globally for pi
-DISABLE_TELEMETRY=1 yes y | npx -y skills add https://github.com/kepano/obsidian-skills \
-  --skill obsidian-markdown --skill obsidian-bases \
-  --skill json-canvas --skill obsidian-cli --skill defuddle \
-  -g -a pi --copy -y
-```
-
-This puts them at `~/.pi/agent/skills/<name>/SKILL.md` where pi
-auto-discovers them. The CLI handles agent detection, symlink/copy,
-and security risk confirmations.
-
-**Verify they're discoverable:**
-
-```bash
-for s in obsidian-markdown obsidian-bases json-canvas obsidian-cli defuddle; do
-  [ -f ~/.pi/agent/skills/$s/SKILL.md ] && echo "✅ $s" || echo "❌ $s"
-done
+pvm setup /path/to/your/vault
 ```
-- `obsidian-markdown` — agent learns Obsidian-flavored markdown syntax
-- `obsidian-bases` — agent learns to generate valid `.base` files (database views)
-- `json-canvas` — agent learns Canvas JSON format (used for our graph sync)
-- `obsidian-cli` — agent learns to use the Obsidian CLI
-- `defuddle` — cleaner markdown extraction from web pages
 
-These skills let the **Miner, Broadcaster, and Heavy-Lifter agents** produce valid Obsidian content.
+The skills live under
+`<vault>/.vault-mind/.pi/agent/skills/<name>/SKILL.md`. `pvm run` disables
+Pi's implicit global/project skill discovery and explicitly loads only these
+curated skills plus skills provided by packages installed in the same
+vault-local agent directory. Do not install these skills globally for a Vault
+Mind session; global copies defeat vault isolation and can create skill-name
+conflicts.
+
+- `obsidian-markdown` — Obsidian-flavored Markdown syntax
+- `obsidian-bases` — valid `.base` database views
+- `json-canvas` — Canvas JSON used by graph sync
+- `obsidian-cli` — Obsidian CLI operation
+- `nlm-skill` — NotebookLM CLI and MCP workflows
+
+These skills let the **Miner, Broadcaster, and Heavy-Lifter agents** produce
+valid Obsidian content without changing the identity of the interactive main
+agent.
 
 ### Built-in Obsidian features used
 

package/dist/src/extension-packages.d.ts

@@ -1,9 +1,9 @@
 /**
- * Canonical list of pi extensions required/optional for vault-mind.
+ * Canonical extension list for the legacy `/vm setup` and Obsidian setup
+ * surfaces. The standalone `pvm` CLI has a broader package-managed runtime
+ * contract in `runtime/pvm-extensions.json`.
  *
- * This is the SINGLE SOURCE OF TRUTH. Shell scripts and the Obsidian plugin
- * consume generated JSON (see scripts/generate-extension-packages-json.mjs).
- * When adding/removing a package, edit ONLY this file and regenerate.
+ * Generate this surface with scripts/generate-extension-packages-json.mjs.
  */
 export declare const PI_REQUIRED_EXTENSIONS: readonly ["npm:pi-vault-mind", "npm:pi-context", "npm:@kylebrodeur/pi-model-discovery", "npm:@kylebrodeur/pi-model-router"];
 export declare const PI_OPTIONAL_EXTENSIONS: readonly ["npm:pi-1password"];

package/dist/src/extension-packages.js

@@ -1,9 +1,9 @@
 /**
- * Canonical list of pi extensions required/optional for vault-mind.
+ * Canonical extension list for the legacy `/vm setup` and Obsidian setup
+ * surfaces. The standalone `pvm` CLI has a broader package-managed runtime
+ * contract in `runtime/pvm-extensions.json`.
  *
- * This is the SINGLE SOURCE OF TRUTH. Shell scripts and the Obsidian plugin
- * consume generated JSON (see scripts/generate-extension-packages-json.mjs).
- * When adding/removing a package, edit ONLY this file and regenerate.
+ * Generate this surface with scripts/generate-extension-packages-json.mjs.
  */
 export const PI_REQUIRED_EXTENSIONS = [
     "npm:pi-vault-mind",

package/dist/test/pvm-setup.test.js

@@ -14,6 +14,7 @@ const requiredExtensions = [
     "npm:@kylebrodeur/pi-model-router",
     "npm:@juicesharp/rpiv-todo@2.7.1",
     "npm:pi-subagents@0.58.0",
+    "git:git@github.com:kylebrodeur/content-writing-system",
 ];
 const runtimeSkills = [
     "obsidian-cli",
@@ -47,6 +48,8 @@ describe("pvm setup", () => {
         fs.writeFileSync(path.join(binDir, "pi"), `#!/usr/bin/env node
 const fs = require("node:fs");
 fs.appendFileSync(process.env.PVM_TEST_PI_LOG, JSON.stringify(process.argv.slice(2)) + "\\n");
+process.stdout.write("NOISY INSTALL STDOUT\\n");
+process.stderr.write("NOISY INSTALL STDERR\\n");
 `, { mode: 0o755 });
         fs.writeFileSync(path.join(binDir, "uv"), `#!/usr/bin/env node
 const fs = require("node:fs");
@@ -121,6 +124,37 @@ fs.appendFileSync(process.env.PVM_TEST_UV_LOG, JSON.stringify(process.argv.slice
         ]) {
             assert.ok(fs.existsSync(path.join(nlmSkillDir, "references", ref)), `nlm-skill reference missing: ${ref}`);
         }
+        assert.doesNotMatch(result.stdout + result.stderr, /NOISY INSTALL/);
+        assert.match(result.stdout, /\[7\/7\] git:git@github\.com:kylebrodeur\/content-writing-system \.\.\. done/);
+        assert.match(result.stdout, /Curated skills \(5\)/);
+    });
+    it("removes package paths that escape the vault-local agent directory", () => {
+        const agentDir = path.join(vaultPath, ".vault-mind", ".pi", "agent");
+        const settingsPath = path.join(agentDir, "settings.json");
+        const insidePackage = path.join(agentDir, "packages", "custom-extension");
+        fs.mkdirSync(insidePackage, { recursive: true });
+        fs.writeFileSync(settingsPath, `${JSON.stringify({
+            packages: ["npm:pi-vault-mind", "../../../../content-writing-system", insidePackage],
+            theme: "dark",
+        }, null, 2)}\n`);
+        const result = runSetup(["--resources-only", vaultPath]);
+        assert.equal(result.status, 0, result.stderr || result.stdout);
+        const settings = JSON.parse(fs.readFileSync(settingsPath, "utf-8"));
+        assert.deepEqual(settings.packages, ["npm:pi-vault-mind", insidePackage]);
+        assert.equal(settings.theme, "dark");
+        assert.match(result.stdout, /Removed 1 external package path/);
+    });
+    it("prints captured installer diagnostics when an extension install fails", () => {
+        fs.writeFileSync(path.join(binDir, "pi"), `#!/usr/bin/env node
+const args = process.argv.slice(2);
+if (args[0] === "install" && args[1] === "npm:pi-context") {
+  process.stderr.write("PI_CONTEXT_INSTALL_FAILED\n");
+  process.exit(23);
+}
+`, { mode: 0o755 });
+        const result = runSetup(["--resources-only", vaultPath]);
+        assert.notEqual(result.status, 0);
+        assert.match(result.stderr + result.stdout, /PI_CONTEXT_INSTALL_FAILED/);
     });
     it("ignores npm exec's transient Pi binary when a stable Pi install is available", () => {
         const transientBin = path.join(testDir, "_npx", "cache-key", "node_modules", ".bin");
@@ -158,6 +192,28 @@ fs.appendFileSync(process.env.PVM_TEST_UV_LOG, JSON.stringify(process.argv.slice
             assert.ok(fs.existsSync(path.join(vaultPath, ".vault-mind", ".pi", "agent", "skills", skill, "SKILL.md")));
         }
     });
+    it("skips extensions already present in the vault settings", () => {
+        const agentDir = path.join(vaultPath, ".vault-mind", ".pi", "agent");
+        fs.mkdirSync(agentDir, { recursive: true });
+        fs.writeFileSync(path.join(agentDir, "settings.json"), `${JSON.stringify({
+            packages: ["npm:pi-vault-mind", "npm:pi-context", "npm:pi-subagents@0.58.0"],
+        })}\n`);
+        const result = runSetup(["--resources-only", vaultPath]);
+        assert.equal(result.status, 0, result.stderr || result.stdout);
+        const installed = installedExtensions();
+        for (const present of ["npm:pi-vault-mind", "npm:pi-context", "npm:pi-subagents@0.58.0"]) {
+            assert.ok(!installed.includes(present), `expected ${present} to be skipped`);
+        }
+        for (const missing of [
+            "npm:@kylebrodeur/pi-model-discovery",
+            "npm:@kylebrodeur/pi-model-router",
+            "npm:@juicesharp/rpiv-todo@2.7.1",
+            "git:git@github.com:kylebrodeur/content-writing-system",
+        ]) {
+            assert.ok(installed.includes(missing), `expected ${missing} to be installed`);
+        }
+        assert.match(result.stdout, /npm:pi-subagents@0\.58\.0 \.\.\. already installed/);
+    });
     it("preserves customized configuration across repeated full setup", () => {
         const first = runSetup([vaultPath]);
         assert.equal(first.status, 0, first.stderr || first.stdout);

package/dist/test/vault-pi-script.test.js

@@ -19,11 +19,21 @@ describe("vault-pi launcher", () => {
         outputPath = path.join(testDir, "pi-output.txt");
         fs.mkdirSync(vaultPath, { recursive: true });
         fs.mkdirSync(binDir, { recursive: true });
+        const skillFiles = [
+            path.join(vaultPath, ".vault-mind", ".pi", "agent", "npm", "node_modules", "@scope", "package", "skills", "scoped-skill", "SKILL.md"),
+            path.join(vaultPath, ".vault-mind", ".pi", "agent", "npm", "node_modules", "pi-context", "skills", "context-management", "SKILL.md"),
+            path.join(vaultPath, ".vault-mind", ".pi", "agent", "skills", "obsidian-cli", "SKILL.md"),
+        ];
+        for (const skillFile of skillFiles) {
+            fs.mkdirSync(path.dirname(skillFile), { recursive: true });
+            fs.writeFileSync(skillFile, "---\nname: test\n---\n");
+        }
         fs.writeFileSync(path.join(binDir, "pi"), `#!/usr/bin/env bash
 set -euo pipefail
 pid_file="$PWD/.vault-mind/.pi/agent/daemon.pid"
-printf 'cwd=%s\nagent=%s\nargs=%s\npid=%s\n' \
-  "$PWD" "$PI_CODING_AGENT_DIR" "$*" "$(cat "$pid_file")" > "$PVM_TEST_OUTPUT"
+printf 'cwd=%s\nagent=%s\npid=%s\n' \
+  "$PWD" "$PI_CODING_AGENT_DIR" "$(cat "$pid_file")" > "$PVM_TEST_OUTPUT"
+printf 'arg=%s\n' "$@" >> "$PVM_TEST_OUTPUT"
 `, { mode: 0o755 });
         for (const command of ["open", "osascript"]) {
             fs.writeFileSync(path.join(binDir, command), "#!/usr/bin/env bash\nexit 97\n", {
@@ -48,10 +58,42 @@ printf 'cwd=%s\nagent=%s\nargs=%s\npid=%s\n' \
         const output = fs.readFileSync(outputPath, "utf-8");
         assert.match(output, new RegExp(`^cwd=${vaultPath.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}$`, "m"));
         assert.match(output, new RegExp(`^agent=${path.join(vaultPath, ".vault-mind", ".pi", "agent").replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}$`, "m"));
-        assert.match(output, /^args=$/m);
+        const args = [...output.matchAll(/^arg=(.*)$/gm)].map((match) => match[1]);
+        const agentDir = path.join(vaultPath, ".vault-mind", ".pi", "agent");
+        assert.deepEqual(args, [
+            "--no-skills",
+            "--no-prompt-templates",
+            "--skill",
+            path.join(agentDir, "npm", "node_modules", "@scope", "package", "skills", "scoped-skill", "SKILL.md"),
+            "--skill",
+            path.join(agentDir, "npm", "node_modules", "pi-context", "skills", "context-management", "SKILL.md"),
+            "--skill",
+            path.join(agentDir, "skills", "obsidian-cli", "SKILL.md"),
+        ]);
         assert.match(output, /^pid=\d+$/m);
         assert.equal(fs.existsSync(path.join(vaultPath, ".vault-mind", ".pi", "agent", "daemon.pid")), false);
     });
+    it("preserves the vault-local 1Password environment flag", () => {
+        const agentDir = path.join(vaultPath, ".vault-mind", ".pi", "agent");
+        fs.mkdirSync(path.join(agentDir, "npm", "node_modules", "pi-1password"), {
+            recursive: true,
+        });
+        fs.mkdirSync(path.join(vaultPath, ".vault-mind"), { recursive: true });
+        fs.writeFileSync(path.join(vaultPath, ".vault-mind", ".env.1pass"), "TOKEN=op://vault/item\n");
+        const result = spawnSync("bash", [launcher, "--same-terminal", vaultPath], {
+            cwd: testDir,
+            encoding: "utf-8",
+            env: {
+                ...process.env,
+                PATH: `${binDir}:${process.env.PATH ?? ""}`,
+                PVM_TEST_OUTPUT: outputPath,
+            },
+        });
+        assert.equal(result.status, 0, result.stderr || result.stdout);
+        const output = fs.readFileSync(outputPath, "utf-8");
+        const args = [...output.matchAll(/^arg=(.*)$/gm)].map((match) => match[1]);
+        assert.deepEqual(args.slice(-2), ["--op-env", ".vault-mind/.env.1pass"]);
+    });
     it("ignores npm exec's transient Pi binary when a stable Pi install is available", () => {
         const transientBin = path.join(testDir, "_npx", "cache-key", "node_modules", ".bin");
         fs.mkdirSync(transientBin, { recursive: true });
@@ -102,6 +144,30 @@ printf 'cwd=%s\nagent=%s\nargs=%s\npid=%s\n' \
         assert.equal(result.status, 97);
         assert.equal(fs.existsSync(outputPath), false);
     });
+    it("passes isolated skill arguments through new-window command construction", () => {
+        for (const command of ["open", "osascript"]) {
+            fs.writeFileSync(path.join(binDir, command), `#!/usr/bin/env node
+const fs = require("node:fs");
+fs.writeFileSync(process.env.PVM_TEST_OUTPUT, JSON.stringify(process.argv.slice(2)));
+`, { mode: 0o755 });
+        }
+        const result = spawnSync("bash", [launcher, "--new-window", vaultPath], {
+            cwd: testDir,
+            encoding: "utf-8",
+            env: {
+                ...process.env,
+                PATH: `${binDir}:${process.env.PATH ?? ""}`,
+                PVM_TEST_OUTPUT: outputPath,
+            },
+        });
+        assert.equal(result.status, 0, result.stderr || result.stdout);
+        const commandText = JSON.parse(fs.readFileSync(outputPath, "utf-8")).join("\n");
+        assert.match(commandText, /--no-skills/);
+        assert.match(commandText, /--no-prompt-templates/);
+        assert.match(commandText, /--skill/);
+        assert.match(commandText, /obsidian-cli/);
+        assert.match(commandText, /SKILL\.md/);
+    });
     it("rejects an unknown launch flag with usage help", () => {
         const result = spawnSync("bash", [launcher, "--new-widnow"], {
             cwd: testDir,

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "pi-vault-mind",
-	"version": "0.16.31",
+	"version": "0.16.33",
 	"packageManager": "pnpm@10.34.5",
 	"description": "Passive Obsidian vault extension for pi. Watches @agent markers, dispatches forked subagents (Miner, Broadcaster, Heavy-Lifter), stores in LanceDB with vector + FTS + graph. Multi-agent 'Drop & Forget' workflow for the pi agent ecosystem.",
 	"main": "dist/index.js",

package/runtime/pvm-extensions.json

@@ -5,7 +5,8 @@
 		"npm:@kylebrodeur/pi-model-discovery",
 		"npm:@kylebrodeur/pi-model-router",
 		"npm:@juicesharp/rpiv-todo@2.7.1",
-		"npm:pi-subagents@0.58.0"
+		"npm:pi-subagents@0.58.0",
+		"git:git@github.com:kylebrodeur/content-writing-system"
 	],
 	"optional": ["npm:pi-1password"]
 }

package/scripts/pvm-setup.mjs

@@ -63,12 +63,18 @@ function commandAvailable(command) {
 	return !result.error && result.status === 0;
 }
 
+function printFailureOutput(result) {
+	if (result.stdout) process.stderr.write(result.stdout);
+	if (result.stderr) process.stderr.write(result.stderr);
+}
+
 function installNotebookLM() {
+	console.log("==> NotebookLM CLI");
 	const versionCheck = spawnSync("nlm", ["--version"], { encoding: "utf-8" });
 	if (!versionCheck.error && versionCheck.status === 0) {
 		const installed = (versionCheck.stdout + versionCheck.stderr).trim();
 		if (installed.includes("0.9.13")) {
-			console.log("==> notebooklm-mcp-cli==0.9.13 already installed, skipping");
+			console.log("    notebooklm-mcp-cli 0.9.13 ... already installed");
 			return;
 		}
 	}
@@ -78,12 +84,15 @@ function installNotebookLM() {
 				"Install uv: https://docs.astral.sh/uv/getting-started/installation/"
 		);
 	}
-	console.log("==> Installing notebooklm-mcp-cli==0.9.13 via uv");
 	const result = spawnSync("uv", ["tool", "install", "--force", "notebooklm-mcp-cli==0.9.13"], {
-		stdio: "inherit",
+		encoding: "utf-8",
 	});
 	if (result.error) fail(`could not start uv: ${result.error.message}`);
-	if (result.status !== 0) process.exit(result.status ?? 1);
+	if (result.status !== 0) {
+		printFailureOutput(result);
+		fail("notebooklm-mcp-cli installation failed", result.status ?? 1);
+	}
+	console.log("    notebooklm-mcp-cli 0.9.13 ... installed");
 }
 
 let piExecutable;
@@ -116,14 +125,17 @@ function resolvePiExecutable() {
 	return piExecutable;
 }
 
-function installExtension(extension, agentDir) {
-	console.log(`    ${extension}`);
+function installExtension(extension, agentDir, index, total) {
 	const result = spawnSync(resolvePiExecutable(), ["install", extension], {
-		stdio: "inherit",
+		encoding: "utf-8",
 		env: { ...process.env, PI_CODING_AGENT_DIR: agentDir },
 	});
 	if (result.error) fail(`could not start pi: ${result.error.message}`);
-	if (result.status !== 0) process.exit(result.status ?? 1);
+	if (result.status !== 0) {
+		printFailureOutput(result);
+		fail(`extension installation failed: ${extension}`, result.status ?? 1);
+	}
+	console.log(`    [${index}/${total}] ${extension} ... done`);
 }
 
 function removeStaleExtension(extension, agentDir) {
@@ -146,16 +158,39 @@ function removeStaleExtensions(agentDir) {
 	for (const extension of STALE_EXTENSIONS) removeStaleExtension(extension, agentDir);
 }
 
+function readInstalledPackages(agentDir) {
+	const settingsPath = path.join(agentDir, "settings.json");
+	try {
+		const settings = JSON.parse(fs.readFileSync(settingsPath, "utf-8"));
+		if (!Array.isArray(settings.packages)) return new Set();
+		return new Set(
+			settings.packages
+				.map((entry) => (typeof entry === "string" ? entry : entry?.source))
+				.filter((source) => typeof source === "string")
+		);
+	} catch {
+		return new Set();
+	}
+}
+
 function installExtensions(agentDir) {
 	const manifest = readExtensionManifest();
-	console.log("==> Installing required Pi extensions");
-	for (const extension of manifest.required) installExtension(extension, agentDir);
+	const extensions = [...manifest.required];
+	if (process.env.PVM_SETUP_SKIP_OPTIONAL !== "1") {
+		for (const extension of manifest.optional) {
+			if (extension === "npm:pi-1password" && !commandAvailable("op")) continue;
+			extensions.push(extension);
+		}
+	}
 
-	if (process.env.PVM_SETUP_SKIP_OPTIONAL === "1") return;
-	for (const extension of manifest.optional) {
-		if (extension === "npm:pi-1password" && !commandAvailable("op")) continue;
-		console.log("==> Installing optional Pi extension");
-		installExtension(extension, agentDir);
+	const installed = readInstalledPackages(agentDir);
+	console.log(`==> Pi extensions (${extensions.length})`);
+	for (const [index, extension] of extensions.entries()) {
+		if (installed.has(extension)) {
+			console.log(`    [${index + 1}/${extensions.length}] ${extension} ... already installed`);
+			continue;
+		}
+		installExtension(extension, agentDir, index + 1, extensions.length);
 	}
 }
 
@@ -163,8 +198,8 @@ function installRuntimeSkills(agentDir) {
 	const sourceRoot = path.join(packageRoot, "runtime", "skills");
 	const destinationRoot = path.join(agentDir, "skills");
 	fs.mkdirSync(destinationRoot, { recursive: true });
-	console.log("==> Installing curated runtime skills");
-	for (const skill of runtimeSkills) {
+	console.log(`==> Curated skills (${runtimeSkills.length})`);
+	for (const [index, skill] of runtimeSkills.entries()) {
 		const source = path.join(sourceRoot, skill);
 		const destination = path.join(destinationRoot, skill);
 		if (!fs.existsSync(path.join(source, "SKILL.md"))) {
@@ -172,8 +207,63 @@ function installRuntimeSkills(agentDir) {
 		}
 		fs.rmSync(destination, { recursive: true, force: true });
 		fs.cpSync(source, destination, { recursive: true });
-		console.log(`    ${skill}`);
+		console.log(`    [${index + 1}/${runtimeSkills.length}] ${skill} ... done`);
+	}
+}
+function isLocalPackagePath(packageSpec) {
+	return (
+		path.isAbsolute(packageSpec) ||
+		packageSpec.startsWith(".") ||
+		packageSpec === "~" ||
+		packageSpec.startsWith(`~${path.sep}`)
+	);
+}
+
+function resolvedPackagePath(packageSpec, agentDir) {
+	const expanded =
+		packageSpec === "~" || packageSpec.startsWith(`~${path.sep}`)
+			? path.join(process.env.HOME ?? "", packageSpec.slice(2))
+			: packageSpec;
+	const resolved = path.resolve(agentDir, expanded);
+	try {
+		return fs.realpathSync(resolved);
+	} catch {
+		return resolved;
+	}
+}
+
+function isWithinDirectory(candidate, directory) {
+	const relative = path.relative(directory, candidate);
+	return relative === "" || (!relative.startsWith(`..${path.sep}`) && !path.isAbsolute(relative));
+}
+
+function sanitizeAgentSettings(agentDir) {
+	const settingsPath = path.join(agentDir, "settings.json");
+	if (!fs.existsSync(settingsPath)) return 0;
+
+	let settings;
+	try {
+		settings = JSON.parse(fs.readFileSync(settingsPath, "utf-8"));
+	} catch (error) {
+		fail(`cannot read ${settingsPath}: ${error instanceof Error ? error.message : String(error)}`);
+	}
+	if (!Array.isArray(settings.packages)) return 0;
+
+	const canonicalAgentDir = fs.realpathSync(agentDir);
+	let removed = 0;
+	settings.packages = settings.packages.filter((packageSpec) => {
+		if (typeof packageSpec !== "string" || !isLocalPackagePath(packageSpec)) return true;
+		const keep = isWithinDirectory(resolvedPackagePath(packageSpec, agentDir), canonicalAgentDir);
+		if (!keep) removed += 1;
+		return keep;
+	});
+	if (removed > 0) {
+		fs.writeFileSync(settingsPath, `${JSON.stringify(settings, null, 2)}\n`, "utf-8");
+		console.log(
+			`==> Removed ${removed} external package path${removed === 1 ? "" : "s"} from vault-local settings`
+		);
 	}
+	return removed;
 }
 
 function scaffoldMainAgentSystem(agentDir, vaultRoot) {
@@ -197,6 +287,7 @@ fs.mkdirSync(agentDir, { recursive: true });
 console.log(`==> Setting up vault-local Pi runtime at ${agentDir}`);
 removeStaleExtensions(agentDir);
 installExtensions(agentDir);
+sanitizeAgentSettings(agentDir);
 installNotebookLM();
 installRuntimeSkills(agentDir);
 

package/scripts/vault-pi.sh

@@ -111,6 +111,28 @@ USE_OP_ENV="false"
 if [ -f "${VAULT}/.vault-mind/.env.1pass" ] && [ -d "${PI_DIR}/npm/node_modules/pi-1password" ]; then
 	USE_OP_ENV="true"
 fi
+# Pi discovers user and project skills even when PI_CODING_AGENT_DIR is vault-local.
+# Disable implicit discovery, then load only curated and installed package skills
+# rooted inside this vault's agent directory.
+PI_ARGS=(--no-skills --no-prompt-templates)
+while IFS= read -r skill_file; do
+	PI_ARGS+=(--skill "${skill_file}")
+done < <(
+	for skills_root in \
+		"${PI_DIR}/skills" \
+		"${PI_DIR}/npm/node_modules"/*/skills \
+		"${PI_DIR}/npm/node_modules"/@*/*/skills; do
+		[ -d "${skills_root}" ] || continue
+		find "${skills_root}" -mindepth 2 -maxdepth 2 -type f -name SKILL.md
+	done | LC_ALL=C sort -u
+)
+
+PI_ARGS_Q=""
+for pi_arg in "${PI_ARGS[@]}"; do
+	printf -v pi_arg_q '%q' "${pi_arg}"
+	PI_ARGS_Q="${PI_ARGS_Q} ${pi_arg_q}"
+done
+
 
 # Auto mode keeps interactive callers, including Obsidian Terminal, in place.
 # Non-interactive runners retain the legacy new-window behavior.
@@ -128,9 +150,9 @@ if [ "${MODE}" = "same-terminal" ]; then
 	cd "${VAULT}"
 	echo "[vault-pi] Starting pi for ${VAULT} in the current terminal"
 	if [ "${USE_OP_ENV}" = "true" ]; then
-		PI_CODING_AGENT_DIR="${PI_DIR}" "${PI_EXECUTABLE}" --op-env .vault-mind/.env.1pass
+		PI_CODING_AGENT_DIR="${PI_DIR}" "${PI_EXECUTABLE}" "${PI_ARGS[@]}" --op-env .vault-mind/.env.1pass
 	else
-		PI_CODING_AGENT_DIR="${PI_DIR}" "${PI_EXECUTABLE}"
+		PI_CODING_AGENT_DIR="${PI_DIR}" "${PI_EXECUTABLE}" "${PI_ARGS[@]}"
 	fi
 	exit $?
 fi
@@ -140,7 +162,7 @@ OP_ENV_ARG=""
 if [ "${USE_OP_ENV}" = "true" ]; then
 	OP_ENV_ARG="--op-env .vault-mind/.env.1pass"
 fi
-PI_CMD="PI_CODING_AGENT_DIR='${PI_DIR}' ${PI_EXECUTABLE_Q} ${OP_ENV_ARG}; rm -f '${PID_FILE}'"
+PI_CMD="PI_CODING_AGENT_DIR='${PI_DIR}' ${PI_EXECUTABLE_Q}${PI_ARGS_Q} ${OP_ENV_ARG}; rm -f '${PID_FILE}'"
 
 if [ -d "/Applications/iTerm.app" ]; then
 	open -a iTerm --args --detach bash -c "echo \$\$ > '${PID_FILE}'; cd '${VAULT}'; ${PI_CMD}"