diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7564c7d7e..7138da67f 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -146,8 +146,8 @@ The codebase is organized into these areas. All are open to contributions:
 | AI/LLM layer | `packages/pi-ai` | Provider integrations, model handling |
 | Agent core | `packages/pi-agent-core` | Agent orchestration — RFC required for changes |
 | Coding agent | `packages/pi-coding-agent` | The main coding agent |
-| MCP server | `packages/mcp-server` | Project state tools and MCP protocol |
 | SF extension | `src/resources/extensions/sf/` | SF workflow — RFC required for auto-mode |
+| MCP client | `src/resources/extensions/mcp-client/` | External MCP tool-server integration only |
 | Other extensions | `src/resources/extensions/` | Browser, search, voice, MCP client, etc. |
 | Native engine | `rust-engine/` | Rust N-API modules (grep, git, AST, etc.) |
 | VS Code extension | `vscode-extension/` | Chat participant, sidebar, RPC integration |
diff --git a/FEATURES.md b/FEATURES.md
index 0666033cb..43917bcbd 100644
--- a/FEATURES.md
+++ b/FEATURES.md
@@ -1,6 +1,6 @@
 # FEATURES
 
-This file is the human-oriented capability map for Singularity Foundry.
+This file is the human-oriented capability map for Singularity Forge.
 
 It is intentionally not the source of truth for schemas or tool parameters. Use it to answer:
 
@@ -11,8 +11,8 @@ It is intentionally not the source of truth for schemas or tool parameters. Use
 For exact contracts, use:
 
 - `README.md` for product positioning and user docs
-- `packages/mcp-server/src/workflow-tools.ts` for workflow tool schemas
-- `src/resources/extensions/sf/` for planning/state-machine behavior
+- `src/resources/extensions/sf/workflow-tools.js` for native workflow tool requirements
+- `src/resources/extensions/sf/` for planning/state-machine behavior and tool schemas
 - `src/resources/extensions/*/extension-manifest.json` for extension inventory
 - `packages/pi-ai/src/` for provider and model registry behavior
 
@@ -22,7 +22,7 @@ SF is a coding-agent application built around:
 
 - a milestone → slice → task planning hierarchy
 - a DB-backed workflow state machine
-- MCP-accessible workflow mutations and readers
+- native SF workflow mutations and readers
 - extension-based capability loading
 - multi-provider model routing
 - interactive and autonomous execution modes
@@ -343,23 +343,32 @@ The section below is generated from source declarations so this overview can sta
 
 <!-- GENERATED_FEATURE_INVENTORY_START -->
 
-### Workflow Tools
+### SF Native Tools
 
-Generated from `packages/mcp-server/src/workflow-tools.ts`.
+Generated from `src/resources/extensions/sf/extension-manifest.json`.
 
+- `sf_autonomous_checkpoint`
 - `sf_complete_milestone`
 - `sf_decision_save`
+- `sf_exec`
+- `sf_exec_search`
+- `sf_graph`
 - `sf_journal_query`
+- `sf_log_judgment`
 - `sf_milestone_generate_id`
 - `sf_milestone_status`
 - `sf_plan_milestone`
 - `sf_plan_slice`
 - `sf_plan_task`
+- `sf_product_audit`
 - `sf_reassess_roadmap`
 - `sf_replan_slice`
 - `sf_requirement_save`
 - `sf_requirement_update`
+- `sf_resume`
 - `sf_save_gate_result`
+- `sf_self_feedback_resolve`
+- `sf_self_report`
 - `sf_skip_slice`
 - `sf_slice_complete`
 - `sf_summary_save`
diff --git a/scripts/generate-features-inventory.mjs b/scripts/generate-features-inventory.mjs
index 39148b8ae..544ea9bf8 100644
--- a/scripts/generate-features-inventory.mjs
+++ b/scripts/generate-features-inventory.mjs
@@ -8,6 +8,7 @@ const repoRoot = resolve(__dirname, "..");
 const featuresPath = join(repoRoot, "FEATURES.md");
 const providersPath = join(repoRoot, "packages", "pi-ai", "src", "types.ts");
 const extensionsRoot = join(repoRoot, "src", "resources", "extensions");
+const sfManifestPath = join(extensionsRoot, "sf", "extension-manifest.json");
 const searchProviderPath = resolveExistingPath(
 	join(
 		repoRoot,
@@ -75,6 +76,19 @@ export function parseBundledExtensions() {
 	return uniqueSorted(entries);
 }
 
+export function parseSfNativeTools() {
+	const manifest = JSON.parse(readFileSync(sfManifestPath, "utf8"));
+	const tools = manifest?.provides?.tools;
+	if (!Array.isArray(tools)) {
+		throw new Error(
+			"Could not find provides.tools in src/resources/extensions/sf/extension-manifest.json",
+		);
+	}
+	return uniqueSorted(
+		tools.filter((tool) => typeof tool === "string" && tool.startsWith("sf_")),
+	);
+}
+
 export function parseSearchProviders() {
 	const src = readFileSync(searchProviderPath, "utf8");
 	const preferencesMatch = src.match(
@@ -100,10 +114,17 @@ function formatBullets(values, formatter = (value) => `- \`${value}\``) {
 
 export function buildSection() {
 	const extensions = parseBundledExtensions();
+	const sfNativeTools = parseSfNativeTools();
 	const searchProviders = parseSearchProviders();
 	const knownProviders = parseKnownProviders();
 
 	return [
+		"### SF Native Tools",
+		"",
+		"Generated from `src/resources/extensions/sf/extension-manifest.json`.",
+		"",
+		formatBullets(sfNativeTools),
+		"",
 		"### Bundled Extensions",
 		"",
 		"Generated from `src/resources/extensions/*/extension-manifest.json`.",
diff --git a/src/tests/features-inventory-generator.test.ts b/src/tests/features-inventory-generator.test.ts
index 40fca8647..788bfc3f2 100644
--- a/src/tests/features-inventory-generator.test.ts
+++ b/src/tests/features-inventory-generator.test.ts
@@ -7,15 +7,22 @@ import {
 	parseBundledExtensions,
 	parseKnownProviders,
 	parseSearchProviders,
+	parseSfNativeTools,
 	START,
 	updateFeaturesContent,
 } from "../../scripts/generate-features-inventory.mjs";
 
-test("features inventory generator surfaces expected workflow tool, extension, search, and provider inventories", () => {
+test("features inventory generator surfaces expected SF native tool, extension, search, and provider inventories", () => {
 	const extensions = parseBundledExtensions();
+	const sfNativeTools = parseSfNativeTools();
 	const searchProviders = parseSearchProviders();
 	const knownProviders = parseKnownProviders();
 
+	assert.ok(sfNativeTools.includes("sf_plan_milestone"));
+	assert.ok(sfNativeTools.includes("sf_task_complete"));
+	assert.ok(sfNativeTools.includes("sf_validate_milestone"));
+	assert.ok(!sfNativeTools.includes("capture_thought"));
+
 	assert.ok(extensions.includes("sf"));
 	assert.ok(extensions.includes("search-the-web"));
 	assert.ok(extensions.includes("subagent"));
@@ -48,13 +55,15 @@ test("features inventory generator injects a rendered appendix between markers",
 	assert.match(
 		updated,
 		new RegExp(
-			`${START.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\n\\n### Bundled Extensions`,
+			`${START.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\n\\n### SF Native Tools`,
 		),
 	);
+	assert.match(updated, /### SF Native Tools/);
 	assert.match(updated, /### Bundled Extensions/);
 	assert.match(updated, /### Search Providers/);
 	assert.match(updated, /### Known Model Providers/);
 	assert.match(updated, /- `search-the-web` — \[extension-manifest\.json]/);
+	assert.match(updated, /- `sf_task_complete`/);
 	assert.match(updated, /- `brave`/);
 	assert.match(updated, /- `xiaomi`/);
 	assert.ok(updated.includes(generated));
diff --git a/vitest.config.ts b/vitest.config.ts
index 8385c0970..9d582966d 100644
--- a/vitest.config.ts
+++ b/vitest.config.ts
@@ -150,10 +150,6 @@ export default defineConfig({
 				__dirname,
 				"packages/native/src/index.ts",
 			),
-			"@singularity-forge/mcp-server": resolve(
-				__dirname,
-				"packages/mcp-server/src/index.ts",
-			),
 			"@singularity-forge/rpc-client": resolve(
 				__dirname,
 				"packages/rpc-client/src/index.ts",
@@ -185,7 +181,6 @@ export default defineConfig({
 			"packages/pi-agent-core/src/**/*.test.ts",
 			"packages/pi-tui/src/**/*.test.ts",
 			"packages/daemon/src/**/*.test.ts",
-			"packages/mcp-server/src/**/*.test.ts",
 			"packages/rpc-client/src/**/*.test.ts",
 			"packages/native/src/**/*.test.mjs",
 			"web/lib/**/*.test.ts",