Add root project dir as a base path in -Xklib-relative-path-base

Previous code didn't work for kotlin-stdlib-wasm because sources from
other gradle projects are included.

`$rootDir/libraries/stdlib/native-wasm/src/*` sources
were present in files.knf as absolute paths. Now they are truncated
as libraries/stdlib/native-wasm/src/*. For example:
libraries/stdlib/native-wasm/src/kotlin/collections/Collections.kt

Should be removed after fixing KT-50876

KTI-729

build.gradle.kts

@@ -496,7 +496,7 @@ allprojects {
         }
 
         val relativePathBaseArg: String? =
-            "-Xklib-relative-path-base=$buildDir,$projectDir".takeIf {
+            "-Xklib-relative-path-base=$buildDir,$projectDir,$rootDir".takeIf {
                 !kotlinBuildProperties.getBoolean("kotlin.build.use.absolute.paths.in.klib")
             }