diff --git a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/ApplyServerSourceAndNmsPatches.kt b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/ApplyServerSourceAndNmsPatches.kt
index d8eaccc..33783df 100644
--- a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/ApplyServerSourceAndNmsPatches.kt
+++ b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/ApplyServerSourceAndNmsPatches.kt
@@ -59,6 +59,10 @@ abstract class ApplyServerSourceAndNmsPatches : BaseTask() {
             if (paperDecompiledSource.isPresent && Files.notExists(nmsFile)) {
                 nmsFile = paperDecompiledSource.file(fileName).get().path
             }
+            if (Files.notExists(nmsFile)) {
+                // we add new files within src/main/resources/data/minecraft/ but they don't exist in the nms source
+                return@forEach
+            }
             val patchFile = patchDir.resolve(fileName).resolveSibling((patchedFile.name + ".patch")) // keep extension
 
             val commandText =
@@ -85,9 +89,9 @@ abstract class ApplyServerSourceAndNmsPatches : BaseTask() {
                 val patchName = patch.name.split("-", limit = 2)[1]
                 println("Applying Patch: $patchName")
                 val excludeArray = directoriesToPatch.get().map { "--exclude=$it/**" }.toTypedArray()
-                git("am", "--ignore-whitespace", *excludeArray, patch.toPath().absolutePathString()).execute()
+                git("am", "--ignore-whitespace", "--include=src/main/resources/data/minecraft/datapacks/paper/**", *excludeArray, "--include=**", patch.toPath().absolutePathString()).execute()
                 val includeArray = directoriesToPatch.get().map { "--include=$it/**" }.toTypedArray()
-                git("apply", "--ignore-whitespace", *includeArray, patch.toPath().absolutePathString()).execute()
+                git("apply", "--ignore-whitespace", "--exclude=src/main/resources/data/minecraft/datapacks/paper/**", *includeArray, patch.toPath().absolutePathString()).execute()
 
                 val (sourceFiles, dataFiles) = McDev.readPatchLines(listOf(patch.toPath()))
                 createPerFileDiff(sourcePatchesDir, sourceFiles, "src/main/java/")
diff --git a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/filterrepo/FinalizePaperHistory.kt b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/filterrepo/FinalizePaperHistory.kt
index 845f137..7d3459e 100644
--- a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/filterrepo/FinalizePaperHistory.kt
+++ b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/mm/filterrepo/FinalizePaperHistory.kt
@@ -32,18 +32,13 @@ abstract class FinalizePaperHistory : BaseTask() {
     @TaskAction
     fun run() {
         Git.checkForGit()
+        val deletionsArr = deletions.get().toTypedArray()
+        if (deletionsArr.isEmpty()) {
+            return
+        }
         Git(paperDir).let { git ->
-            val paperMojangApi = outputDir.path.resolve("Paper-MojangAPI/src/main/java")
-            paperMojangApi.copyRecursivelyTo(outputDir.path.resolve("paper-api/src/main/java"))
-            paperMojangApi.deleteRecursive()
-            git("add", "paper-api/src/main/java", "Paper-MojangAPI").execute()
-            git("commit", "--message", "Merge Paper-MojangAPI into Paper API", "--author=Automated <auto@mated.null>").execute()
-
-            val deletionsArr = deletions.get().toTypedArray()
-            if (deletionsArr.isNotEmpty()) {
-                git("rm", "-r", *deletionsArr).execute()
-                git("commit", "-m", "OWW! That fork is HARD!", "--author=Automated <auto@mated.null>").execute()
-            }
+            git("rm", "-r", *deletionsArr).execute()
+            git("commit", "-m", "OWW! That fork is HARD!", "--author=Automated <auto@mated.null>").execute()
         }
     }
 }