diff --git a/tools/mcmanifest.js b/tools/mcmanifest.js
index 6ef9e4668..5e8e55128 100644
--- a/tools/mcmanifest.js
+++ b/tools/mcmanifest.js
@@ -2989,7 +2989,15 @@ export class Tool extends TOOL {
 						this.environment[name] = `${this.environment[name]} ${value}`;
 				}
 				else {
-					if (typeof value == "string") {
+					// If the shell already provides this variable and it hasn't been set
+					// by the tool internally, prefer the shell value over the manifest
+					// default so user-configured paths (e.g. xs-dev install locations)
+					// are not overridden by the manifest's default assumptions.
+					const shellValue = this.getenv(name);
+					if (shellValue !== undefined && !(name in this.environment)) {
+						value = shellValue;
+					}
+					else if (typeof value == "string") {
 						const dotSlash = "." + this.slash;
 						value = this.resolveVariable(value);
 						if (value.startsWith(dotSlash)) {
diff --git a/tools/mcpack.js b/tools/mcpack.js
index 91813a3f1..e00c7fbf5 100644
--- a/tools/mcpack.js
+++ b/tools/mcpack.js
@@ -1043,10 +1043,12 @@ export default class extends TOOL {
 	}
 	includeManifest(include, from, directory) {
 		this.currentDirectory = directory;
-		let path = this.resolveFilePath(this.resolveVariable(include));
-		if (!path)
-			throw new Error("'" + include + "': manifest not found!");
-		this.parseManifest(path, from);
+		if ("string" == typeof include) {
+			let path = this.resolveFilePath(this.resolveVariable(include));
+			if (!path)
+				throw new Error("'" + include + "': manifest not found!");
+			this.parseManifest(path, from);
+		}
 	}
 	mapBuiltins(builtins) {
 		const map = new Map;
@@ -1080,7 +1082,15 @@ export default class extends TOOL {
 		if (properties) {
 			for (let name in properties) {
 				let value = properties[name];
-				if (typeof value == "string") {
+				// If the shell already provides this variable and it hasn't been set
+				// by the tool internally, prefer the shell value over the manifest
+				// default so user-configured paths (e.g. xs-dev install locations)
+				// are not overridden by the manifest's default assumptions.
+				const shellValue = this.getenv(name);
+				if (shellValue !== undefined && !(name in this.environment)) {
+					value = shellValue;
+				}
+				else if (typeof value == "string") {
 					const dotSlash = "." + this.slash;
 					value = this.resolveVariable(value);
 					if (value.startsWith(dotSlash)) {
@@ -1092,10 +1102,8 @@ export default class extends TOOL {
 								value = path + value.slice(1);
 						}
 					}
-					this.environment[name] = value;
 				}
-				else
-					this.environment[name] = value;
+				this.environment[name] = value;
 			}
 		}
 	}