diff --git a/src/resources/extensions/mcp-client/index.ts b/src/resources/extensions/mcp-client/index.ts
index 2ed6b7729..f29a46175 100644
--- a/src/resources/extensions/mcp-client/index.ts
+++ b/src/resources/extensions/mcp-client/index.ts
@@ -24,6 +24,7 @@ import { Client } from "@modelcontextprotocol/sdk/client";
 import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
 import { StreamableHTTPClientTransport } from "@modelcontextprotocol/sdk/client/streamableHttp.js";
 import { readFileSync, existsSync } from "node:fs";
+import { homedir } from "node:os";
 import { join } from "node:path";
 import { buildHttpTransportOpts } from "./auth.js";
 import type { McpHttpAuthConfig } from "./auth.js";
@@ -66,9 +67,15 @@ function readConfigs(): McpServerConfig[] {
 
 	const servers: McpServerConfig[] = [];
 	const seen = new Set<string>();
+	// Search order matters: first hit wins (seen-guard below), so put
+	// project-local configs first — a project can override or shadow a
+	// globally-registered server by re-declaring the same name.
+	const sfHome = process.env.SF_HOME || join(homedir(), ".sf");
 	const configPaths = [
 		join(process.cwd(), ".mcp.json"),
 		join(process.cwd(), ".sf", "mcp.json"),
+		join(sfHome, "mcp.json"),            // global: ~/.sf/mcp.json
+		join(sfHome, "agent", "mcp.json"),   // global: ~/.sf/agent/mcp.json (legacy alt)
 	];
 
 	for (const configPath of configPaths) {
diff --git a/src/resources/extensions/sf/preferences.ts b/src/resources/extensions/sf/preferences.ts
index 8210bf3ef..bc0672af1 100644
--- a/src/resources/extensions/sf/preferences.ts
+++ b/src/resources/extensions/sf/preferences.ts
@@ -12,7 +12,7 @@
 
 import { existsSync, readFileSync } from "node:fs";
 import { homedir } from "node:os";
-import { join } from "node:path";
+import { join, dirname, resolve } from "node:path";
 
 import { sfRoot } from "./paths.js";
 import { parse as parseYaml } from "yaml";
@@ -110,8 +110,46 @@ function legacyGlobalPreferencesPath(): string {
   return join(homedir(), ".pi", "agent", "sf-preferences.md");
 }
 
+/**
+ * Resolve the "project root" for preferences. When SF is running inside a
+ * git worktree (e.g. `.sf/worktrees/M003/`), project-level prefs should
+ * come from the MAIN worktree's `.sf/PREFERENCES.md`, not the milestone
+ * branch's frozen copy. Otherwise a pref change on main never reaches an
+ * in-flight milestone, and we saw this in practice: updating PREFERENCES
+ * on main had no effect until the milestone branch merged main.
+ *
+ * Strategy: read `.git` in the current worktree. If it's a file of the
+ * form `gitdir: <path>`, we're in a linked worktree — resolve the
+ * commondir and walk up one level to reach the main worktree. Fall back
+ * to cwd silently for non-worktree setups (bare clones, submodules, etc.
+ * where the current logic is already correct).
+ */
+function projectPrefsRoot(): string {
+  const cwd = process.cwd();
+  try {
+    const gitPath = join(cwd, ".git");
+    if (!existsSync(gitPath)) return cwd;
+    const stat = readFileSync(gitPath, "utf-8");
+    // Linked worktrees have `.git` as a FILE: "gitdir: /abs/path/to/main/.git/worktrees/NAME"
+    const m = /^gitdir:\s*(.+)$/m.exec(stat.trim());
+    if (!m) return cwd;
+    const gitdir = m[1].trim();
+    // gitdir looks like /.../.git/worktrees/NAME — commondir is the /.../.git/ part;
+    // the main worktree is the directory containing that .git dir.
+    // Use the `commondir` pointer file inside the linked worktree's gitdir when present.
+    const commondirFile = join(gitdir, "commondir");
+    if (existsSync(commondirFile)) {
+      const rel = readFileSync(commondirFile, "utf-8").trim();
+      const commondir = resolve(gitdir, rel);  // usually "../.." → /.../.git
+      const mainRoot = dirname(commondir);      // /.../ (main worktree root)
+      if (existsSync(join(mainRoot, ".sf"))) return mainRoot;
+    }
+  } catch { /* non-fatal — fall back to cwd */ }
+  return cwd;
+}
+
 function projectPreferencesPath(): string {
-  return join(sfRoot(process.cwd()), "preferences.md");
+  return join(sfRoot(projectPrefsRoot()), "preferences.md");
 }
 // Bootstrap in gitignore.ts historically created PREFERENCES.md (uppercase) by mistake.
 // Check uppercase as a fallback so those files aren't silently ignored.
@@ -119,7 +157,7 @@ function globalPreferencesPathUppercase(): string {
   return join(sfHome(), "PREFERENCES.md");
 }
 function projectPreferencesPathUppercase(): string {
-  return join(sfRoot(process.cwd()), "PREFERENCES.md");
+  return join(sfRoot(projectPrefsRoot()), "PREFERENCES.md");
 }
 
 export function getGlobalSFPreferencesPath(): string {