diff --git a/buildSrc/src/main/kotlin/task/ApplyPatches.kt b/buildSrc/src/main/kotlin/task/ApplyPatches.kt
index f158c51f..8dca4d41 100644
--- a/buildSrc/src/main/kotlin/task/ApplyPatches.kt
+++ b/buildSrc/src/main/kotlin/task/ApplyPatches.kt
@@ -102,13 +102,37 @@ internal fun Project.createApplyPatchesTask(
     }
 
     fun initYarn() { // Todo actually port to kotlin
-        val paperDecompDir = toothpick.paperDecompDir
         bashCmd("cd mappings/mapper && ./gradlew installDist", printOut = true)
         bashCmd("rm -fr mappings/work/Base", printOut = true)
         bashCmd("mkdir -p mappings/work/Base/src/main/java/com/mojang", printOut = true)
-        bashCmd("cp -r $paperDecompDir/spigot/* mappings/work/Base/src/main/java/", printOut = true, dir = project.getRootDir())
+        bashCmd("cp -r ${toothpick.paperDecompDir}/spigot/* mappings/work/Base/src/main/java/", printOut = true)
+
+        // Todo start - make this code better
+        val patchPaths = Files.newDirectoryStream(Paths.get("${rootProject.projectDir}/patches/server"))
+            .map { it.toFile() }
+            .filter { it.name.endsWith(".patch") }
+            .sorted()
+            .toList()
+
+        val linesRaw = patchPaths.asSequence()
+            .flatMap { it.readLines().asSequence() }
+
+        val lines = linesRaw
+            .filter { line -> line.startsWith("--- a/src/main/java/") && !linesRaw.contains("+++ b/${line.substringAfter("""-- a/""")}") }
+            .toList().distinct()
+
+        val removedFiles = lines.asSequence()
+            .filter { line -> line.startsWith("--- a/src/main/java/") }
+            .distinct()
+            .map { it.substringAfter("/src/main/java/") }
+            .toSet()
+        // Todo end
+
         bashCmd("cp -r $forkName-Server/src/main/java/* mappings/work/Base/src/main/java/", printOut = true)
-        bashCmd("cp -r $paperDecompDir/libraries/com.mojang/*/* mappings/work/Base/src/main/java/", printOut = true)
+        bashCmd("cp -r ${toothpick.paperDecompDir}/libraries/com.mojang/*/* mappings/work/Base/src/main/java/", printOut = true)
+
+        removedFiles.forEach{ bashCmd("rm -frv mappings/work/Base/src/main/java/$it", printOut = true) }
+
         bashCmd("rm -fr mappings/work/$forkName-Server_yarn_unpatched && mkdir -p mappings/work/$forkName-Server_yarn_unpatched/src/main/java", printOut = true)
         bashCmd("cp $forkName-Server/.gitignore $forkName-Server/pom.xml $forkName-Server/checkstyle.xml $forkName-Server/CONTRIBUTING.md $forkName-Server/LGPL.txt $forkName-Server/LICENCE.txt $forkName-Server/README.md mappings/work/$forkName-Server_yarn_unpatched/", printOut = true)
         bashCmd("JAVA_OPTS='-Xms1G -Xmx2G' mappings/mapper/build/install/mapper/bin/mapper mappings/map.srg mappings/work/Base/src/main/java mappings/work/$forkName-Server_yarn_unpatched/src/main/java", printOut = true)
diff --git a/mappings/scripts/install.sh b/mappings/scripts/install.sh
index 654d8b30..e1bd8f13 100755
--- a/mappings/scripts/install.sh
+++ b/mappings/scripts/install.sh
@@ -13,26 +13,29 @@ do_fixes(){
 git config init.defaultBranch master
 
 cd $basedir/mappings/work
-rm -fr Yatopia-Server_remapped
-mkdir -p Yatopia-Server_remapped/src/main
-cp -r Base/src/main/java Yatopia-Server_remapped/src/main/
-cd Yatopia-Server_remapped
+rm -fr "${inputdirprefix}Server_remapped"
+mkdir -p "${inputdirprefix}Server_remapped/src/main"
+cp -r Base/src/main/java "${inputdirprefix}Server_remapped/src/main/"
+cd "${inputdirprefix}Server_remapped"
 git init
 git add .
 git commit --quiet --message=Base
 rm -fr src/main/java/*
 cd ..
-JAVA_OPTS="-Xms1G -Xmx2G" "${basedir}/mappings/mapper/build/install/mapper/bin/mapper" "${basedir}/mappings/unmap.srg" "${basedir}/Yatopia-Server_yarn/src/main/java" "${basedir}/mappings/work/Yatopia-Server_remapped/src/main/java"
+JAVA_OPTS="-Xms1G -Xmx2G" "${basedir}/mappings/mapper/build/install/mapper/bin/mapper" "${basedir}/mappings/unmap.srg" "${basedir}/${inputdirprefix}Server_yarn/src/main/java" "${basedir}/mappings/work/${inputdirprefix}Server_remapped/src/main/java"
 
 
-cd ${basedir}/mappings/work/Yatopia-Server_remapped/src/main/java
+cd "${basedir}/mappings/work/${inputdirprefix}Server_remapped/src/main/java"
 do_fixes
 
 cd "$basedir"
-changed="$(cat mappedPatches/*.patch | grep "+++ b/" | sort | uniq | sed 's/\+\+\+ b\///g')"
-cd ${basedir}/mappings/work/Yatopia-Server_remapped
+changed="$(cat mappedPatches/*.patch | grep "+++ b/\|+++ a/\|--- b/\|--- a/" | sort | uniq | sed 's/\+\+\+ b\///g' | sed 's/\+\+\+ a\///g' | sed 's/\-\-\- b\///g' | sed 's/\-\-\- a\///g')"
+cd "${basedir}/mappings/work/${inputdirprefix}Server_remapped"
 # git add .
-git add $changed #only commit the files that were modified
+for file in $changed; do
+    git add $file || true
+done
+# git add $changed #only commit the files that were modified
 git diff --cached > a.patch
 
 
@@ -46,6 +49,6 @@ if [ $(git log --pretty=format:'%s' | grep '<Mapped Patches>' | wc -l) != "0" ];
     fi
 fi
 
-patch -p1 < "$basedir/mappings/work/Yatopia-Server_remapped/a.patch"
+patch -p1 < "$basedir/mappings/work/${inputdirprefix}Server_remapped/a.patch"
 git add .
 git commit -m "<Mapped Patches>"