diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/CoreTasks.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/CoreTasks.kt
index 057511ca4..3f2891080 100644
--- a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/CoreTasks.kt
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/CoreTasks.kt
@@ -28,6 +28,7 @@ import io.papermc.paperweight.core.tasks.ImportLibraryFiles
 import io.papermc.paperweight.core.tasks.IndexLibraryFiles
 import io.papermc.paperweight.core.tasks.SetupMinecraftSources
 import io.papermc.paperweight.core.tasks.SetupPaperScript
+import io.papermc.paperweight.core.tasks.patching.ProcessNewSourceATs
 import io.papermc.paperweight.core.util.coreExt
 import io.papermc.paperweight.tasks.*
 import io.papermc.paperweight.tasks.mache.DecompileJar
@@ -40,6 +41,8 @@ import org.gradle.api.Project
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.TaskContainer
 import org.gradle.kotlin.dsl.*
+import org.gradle.kotlin.dsl.provideDelegate
+import org.gradle.kotlin.dsl.registering
 
 class CoreTasks(
     val project: Project,
@@ -153,6 +156,16 @@ class CoreTasks(
 
                 root.set(project.rootProject.layout.projectDirectory)
             }
+
+            val processNewSourceATs by project.tasks.registering(ProcessNewSourceATs::class) {
+                description = "Processes new source ATs"
+
+                base.set(layout.cache.resolve(BASE_PROJECT).resolve("sources"))
+                input.set(layout.projectDirectory.dir("src/minecraft/java"))
+                atFile.set(project.coreExt.paper.additionalAts.fileExists(project))
+                ats.jstClasspath.from(project.configurations.named(MACHE_MINECRAFT_CONFIG))
+                ats.jst.from(project.configurations.named(JST_CONFIG))
+            }
         }
 
         // Setup Paper's Minecraft patching tasks
diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/MinecraftPatchingTasks.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/MinecraftPatchingTasks.kt
index 5fe4bf9af..d2b04268d 100644
--- a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/MinecraftPatchingTasks.kt
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/taskcontainers/MinecraftPatchingTasks.kt
@@ -206,11 +206,6 @@ class MinecraftPatchingTasks(
             input.set(outputSrc)
             patches.set(sourcePatchDir)
             gitFilePatches.set(this@MinecraftPatchingTasks.gitFilePatches)
-
-            ats.jstClasspath.from(project.configurations.named(MACHE_MINECRAFT_CONFIG))
-            ats.jst.from(project.configurations.named(JST_CONFIG))
-            atFile.set(additionalAts.fileExists(project))
-            atFileOut.set(additionalAts.fileExists(project))
         }
 
         val rebuildResourcePatches = tasks.register<RebuildFilePatches>(rebuildResourcePatchesName) {
diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/SetupMinecraftSources.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/SetupMinecraftSources.kt
index 673970b2c..e1ccec282 100644
--- a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/SetupMinecraftSources.kt
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/SetupMinecraftSources.kt
@@ -28,6 +28,7 @@ import codechicken.diffpatch.util.archiver.ArchiveFormat
 import io.papermc.paperweight.core.util.ApplySourceATs
 import io.papermc.paperweight.tasks.*
 import io.papermc.paperweight.util.*
+import io.papermc.paperweight.util.constants.*
 import java.nio.file.Path
 import java.util.function.Predicate
 import kotlin.io.path.*
@@ -81,7 +82,7 @@ abstract class SetupMinecraftSources : JavaLauncherTask() {
         val git: Git
         if (outputPath.resolve(".git/HEAD").isRegularFile()) {
             git = Git.open(outputPath.toFile())
-            git.reset().setRef("ROOT").setMode(ResetCommand.ResetType.HARD).call()
+            git.reset().setRef(MACHE_TAG_ROOT).setMode(ResetCommand.ResetType.HARD).call()
         } else {
             outputPath.createDirectories()
 
@@ -90,10 +91,10 @@ abstract class SetupMinecraftSources : JavaLauncherTask() {
                 .setInitialBranch("main")
                 .call()
 
-            val rootIdent = PersonIdent("ROOT", "noreply+automated@papermc.io")
-            git.commit().setMessage("ROOT").setAllowEmpty(true).setAuthor(rootIdent).setSign(false).call()
-            git.tagDelete().setTags("ROOT").call()
-            git.tag().setName("ROOT").setTagger(rootIdent).setSigned(false).call()
+            val rootIdent = PersonIdent(MACHE_TAG_ROOT, "noreply+automated@papermc.io")
+            git.commit().setMessage(MACHE_TAG_ROOT).setAllowEmpty(true).setAuthor(rootIdent).setSign(false).call()
+            git.tagDelete().setTags(MACHE_TAG_ROOT).call()
+            git.tag().setName(MACHE_TAG_ROOT).setTagger(rootIdent).setSigned(false).call()
         }
 
         if (macheOld.isPresent) {
@@ -130,7 +131,7 @@ abstract class SetupMinecraftSources : JavaLauncherTask() {
         println("Setup git repo...")
         if (!macheOld.isPresent) {
             // skip this if we are diffing against old, since it would be a commit without mache patches
-            commitAndTag(git, "Vanilla")
+            commitAndTag(git, MACHE_TAG_VANILLA)
         }
 
         if (!mache.isEmpty) {
@@ -147,7 +148,7 @@ abstract class SetupMinecraftSources : JavaLauncherTask() {
                 .build()
                 .operate()
 
-            commitAndTag(git, "Mache")
+            commitAndTag(git, MACHE_TAG_PATCHES)
 
             if (result.exit != 0) {
                 throw Exception("Failed to apply ${result.summary.failedMatches} mache patches")
@@ -165,13 +166,13 @@ abstract class SetupMinecraftSources : JavaLauncherTask() {
                 atFile.path,
                 temporaryDir.toPath(),
             )
-            commitAndTag(git, "ATs", "paper ATs")
+            commitAndTag(git, MACHE_TAG_ATS, "paper ATs")
         }
 
         if (libraryImports.isPresent) {
             libraryImports.path.copyRecursivelyTo(outputPath)
 
-            commitAndTag(git, "Imports", "paper Imports")
+            commitAndTag(git, MACHE_TAG_IMPORTS, "paper Imports")
         }
 
         git.close()
diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFeaturePatches.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFeaturePatches.kt
index 1e5a51c5b..2bcd3af1a 100644
--- a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFeaturePatches.kt
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFeaturePatches.kt
@@ -25,8 +25,10 @@ package io.papermc.paperweight.core.tasks.patching
 import io.papermc.paperweight.PaperweightException
 import io.papermc.paperweight.tasks.*
 import io.papermc.paperweight.util.*
+import io.papermc.paperweight.util.constants.*
 import java.nio.file.Path
 import kotlin.io.path.*
+import kotlin.io.path.createDirectories
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
@@ -86,7 +88,7 @@ abstract class ApplyFeaturePatches : ControllableOutputTask() {
         if (git("checkout", "main").runSilently(silenceErr = true) != 0) {
             git("checkout", "-b", "main").runSilently(silenceErr = true)
         }
-        git("reset", "--hard", "file").executeSilently(silenceErr = true)
+        git("reset", "--hard", MACHE_TAG_FILE).executeSilently(silenceErr = true)
         git("gc").runSilently(silenceErr = true)
 
         applyGitPatches(git, "server repo", repoPath, patches.path, printOutput.get(), verbose.get())
diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFilePatches.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFilePatches.kt
index 7f692b392..efdfa7671 100644
--- a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFilePatches.kt
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ApplyFilePatches.kt
@@ -28,6 +28,7 @@ import codechicken.diffpatch.util.LoggingOutputStream
 import codechicken.diffpatch.util.PatchMode
 import io.papermc.paperweight.tasks.*
 import io.papermc.paperweight.util.*
+import io.papermc.paperweight.util.constants.*
 import java.io.PrintStream
 import java.nio.file.Path
 import java.time.Instant
@@ -202,8 +203,8 @@ abstract class ApplyFilePatches : BaseTask() {
             .setAllowEmpty(true)
             .setSign(false)
             .call()
-        git.tagDelete().setTags("file").call()
-        git.tag().setName("file").setTagger(ident).setSigned(false).call()
+        git.tagDelete().setTags(MACHE_TAG_FILE).call()
+        git.tag().setName(MACHE_TAG_FILE).setTagger(ident).setSigned(false).call()
         git.close()
     }
 
diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/FixupFilePatches.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/FixupFilePatches.kt
index 52a7cdecb..6180c3695 100644
--- a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/FixupFilePatches.kt
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/FixupFilePatches.kt
@@ -24,6 +24,7 @@ package io.papermc.paperweight.core.tasks.patching
 
 import io.papermc.paperweight.tasks.*
 import io.papermc.paperweight.util.*
+import io.papermc.paperweight.util.constants.*
 import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.Input
@@ -44,7 +45,7 @@ abstract class FixupFilePatches : BaseTask() {
     fun run() {
         val git = Git(repo)
         git("add", ".").executeOut()
-        git("commit", "--fixup", "file").executeOut()
+        git("commit", "--fixup", MACHE_TAG_FILE).executeOut()
         git("-c", "sequence.editor=:", "rebase", "-i", "--autosquash", upstream.get()).executeOut()
     }
 }
diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ProcessNewSourceATs.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ProcessNewSourceATs.kt
new file mode 100644
index 000000000..dcfb9932c
--- /dev/null
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/ProcessNewSourceATs.kt
@@ -0,0 +1,184 @@
+/*
+ * paperweight is a Gradle plugin for the PaperMC project.
+ *
+ * Copyright (c) 2023 Kyle Wood (DenWav)
+ *                    Contributors
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation;
+ * version 2.1 only, no later versions.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
+ * USA
+ */
+
+package io.papermc.paperweight.core.tasks.patching
+
+import io.papermc.paperweight.PaperweightException
+import io.papermc.paperweight.core.util.ApplySourceATs
+import io.papermc.paperweight.tasks.*
+import io.papermc.paperweight.util.*
+import io.papermc.paperweight.util.constants.*
+import java.nio.file.Path
+import kotlin.io.path.*
+import org.cadixdev.at.AccessTransformSet
+import org.cadixdev.at.io.AccessTransformFormats
+import org.cadixdev.bombe.type.signature.MethodSignature
+import org.gradle.api.file.DirectoryProperty
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.InputFile
+import org.gradle.api.tasks.Nested
+import org.gradle.api.tasks.Optional
+import org.gradle.api.tasks.TaskAction
+import org.gradle.api.tasks.UntrackedTask
+import org.gradle.kotlin.dsl.*
+
+@UntrackedTask(because = "Always process when requested")
+abstract class ProcessNewSourceATs : JavaLauncherTask() {
+
+    @get:InputDirectory
+    abstract val input: DirectoryProperty
+
+    @get:InputDirectory
+    abstract val base: DirectoryProperty
+
+    @get:Optional
+    @get:InputFile
+    abstract val atFile: RegularFileProperty
+
+    @get:Nested
+    val ats: ApplySourceATs = objects.newInstance()
+
+    @TaskAction
+    fun run() {
+        val inputDir = input.convertToPath()
+        val baseDir = base.convertToPath()
+
+        // find ATs, cleanup comment, apply to base
+        val newATs = handleAts(baseDir, inputDir, atFile)
+
+        // save work and jump to AT commit
+        val git = Git(inputDir)
+        git("stash", "push").executeSilently(silenceErr = true)
+        git("checkout", MACHE_TAG_ATS).executeSilently(silenceErr = true)
+
+        // apply new ATs to source
+        newATs.forEach { (path, ats) ->
+            val source = inputDir.resolve(path)
+            applyNewATs(source, ats)
+        }
+
+        // commit new ATs
+        git("add", ".").executeSilently(silenceErr = true)
+        git("commit", "--amend", "--no-edit").executeSilently(silenceErr = true)
+
+        // clean up tree: rebasing drops the old AT commit and replaces it with the new one
+        git("switch", "-").executeSilently(silenceErr = true)
+        git("rebase", MACHE_TAG_ATS).executeOut()
+
+        git("stash", "pop").executeSilently(silenceErr = true)
+    }
+
+    private fun handleAts(
+        baseDir: Path,
+        inputDir: Path,
+        atFile: RegularFileProperty
+    ): MutableList<Pair<String, AccessTransformSet>> {
+        val oldAts = AccessTransformFormats.FML.read(atFile.path)
+        val newATs = mutableListOf<Pair<String, AccessTransformSet>>()
+
+        baseDir.walk()
+            .map { it.relativeTo(baseDir).invariantSeparatorsPathString }
+            .filter { it.endsWith(".java") }
+            .forEach {
+                val ats = AccessTransformSet.create()
+                val source = inputDir.resolve(it)
+                val decomp = baseDir.resolve(it)
+                val className = it.replace(".java", "")
+                if (findATInSource(source, ats, className)) {
+                    applyNewATs(decomp, ats)
+                    newATs.add(it to ats)
+                }
+                oldAts.merge(ats)
+            }
+
+        AccessTransformFormats.FML.writeLF(
+            atFile.path,
+            oldAts,
+            "# This file is auto generated, any changes may be overridden!\n# See CONTRIBUTING.md on how to add access transformers.\n"
+        )
+
+        return newATs
+    }
+
+    private fun applyNewATs(decomp: Path, newAts: AccessTransformSet) {
+        if (newAts.classes.isEmpty()) {
+            return
+        }
+
+        val at = temporaryDir.toPath().resolve("ats.cfg").createParentDirectories()
+        AccessTransformFormats.FML.writeLF(at, newAts)
+        ats.run(
+            launcher.get(),
+            decomp,
+            decomp,
+            at,
+            temporaryDir.toPath().resolve("jst_work").cleanDir(),
+            singleFile = true,
+        )
+    }
+
+    private fun findATInSource(source: Path, newAts: AccessTransformSet, className: String): Boolean {
+        if (!source.exists()) {
+            // source was added via lib imports
+            return false
+        }
+
+        val sourceLines = source.readLines()
+        var foundNew = false
+        val fixedLines = ArrayList<String>(sourceLines.size)
+        sourceLines.forEach { line ->
+            if (!line.contains("// Paper-AT: ")) {
+                fixedLines.add(line)
+                return@forEach
+            }
+
+            foundNew = true
+
+            val split = line.split("// Paper-AT: ")
+            val at = split[1]
+            try {
+                val atClass = newAts.getOrCreateClass(className)
+                val parts = at.split(" ")
+                val accessTransform = atFromString(parts[0])
+                val name = parts[1]
+                val index = name.indexOf('(')
+                if (index == -1) {
+                    atClass.mergeField(name, accessTransform)
+                } else {
+                    atClass.mergeMethod(MethodSignature.of(name.substring(0, index), name.substring(index)), accessTransform)
+                }
+                logger.lifecycle("Found new AT in $className: $at -> $accessTransform")
+            } catch (ex: Exception) {
+                throw PaperweightException("Found invalid AT '$at' in class $className")
+            }
+
+            fixedLines.add(split[0].trimEnd())
+        }
+
+        if (foundNew) {
+            source.writeText(fixedLines.joinToString("\n", postfix = "\n"), Charsets.UTF_8)
+        }
+
+        return foundNew
+    }
+}
diff --git a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatches.kt b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatches.kt
index 68c016b1d..b764f8324 100644
--- a/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatches.kt
+++ b/paperweight-core/src/main/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatches.kt
@@ -25,23 +25,17 @@ package io.papermc.paperweight.core.tasks.patching
 import codechicken.diffpatch.cli.DiffOperation
 import codechicken.diffpatch.util.LogLevel
 import codechicken.diffpatch.util.LoggingOutputStream
-import io.papermc.paperweight.PaperweightException
-import io.papermc.paperweight.core.util.ApplySourceATs
 import io.papermc.paperweight.tasks.*
 import io.papermc.paperweight.util.*
+import io.papermc.paperweight.util.constants.*
 import java.io.PrintStream
 import java.nio.file.Path
 import kotlin.io.path.*
-import org.cadixdev.at.AccessTransformSet
-import org.cadixdev.at.io.AccessTransformFormats
-import org.cadixdev.bombe.type.signature.MethodSignature
 import org.gradle.api.file.DirectoryProperty
-import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.provider.Property
 import org.gradle.api.tasks.*
 import org.gradle.api.tasks.options.Option
 import org.gradle.kotlin.dsl.*
-import org.intellij.lang.annotations.Language
 
 @UntrackedTask(because = "Always rebuild patches")
 abstract class RebuildFilePatches : JavaLauncherTask() {
@@ -62,14 +56,6 @@ abstract class RebuildFilePatches : JavaLauncherTask() {
     @get:OutputDirectory
     abstract val patches: DirectoryProperty
 
-    @get:Optional
-    @get:InputFile
-    abstract val atFile: RegularFileProperty
-
-    @get:Optional
-    @get:OutputFile
-    abstract val atFileOut: RegularFileProperty
-
     @get:Input
     abstract val contextLines: Property<Int>
 
@@ -77,9 +63,6 @@ abstract class RebuildFilePatches : JavaLauncherTask() {
     @get:Input
     abstract val gitFilePatches: Property<Boolean>
 
-    @get:Nested
-    val ats: ApplySourceATs = objects.newInstance()
-
     override fun init() {
         super.init()
         contextLines.convention(3)
@@ -95,28 +78,8 @@ abstract class RebuildFilePatches : JavaLauncherTask() {
 
         val git = Git(inputDir)
         git("stash", "push").executeSilently(silenceErr = true)
-        git("checkout", "file").executeSilently(silenceErr = true)
+        git("checkout", MACHE_TAG_FILE).executeSilently(silenceErr = true)
 
-        val filesWithNewAts = if (!ats.jst.isEmpty) {
-            handleAts(
-                baseDir,
-                inputDir,
-                atFile,
-                atFileOut,
-            )
-        } else {
-            emptyList()
-        }
-
-        if (filesWithNewAts.isNotEmpty()) {
-            git("status").executeOut()
-            git("diff").executeOut()
-            // we removed the comment, we need to commit this
-            git("add", ".").executeOut()
-            git("commit", "--amend", "--no-edit").executeOut()
-        }
-
-        // rebuild patches
         val result = if (gitFilePatches.get()) {
             rebuildWithGit(git, patchDir)
         } else {
@@ -124,29 +87,10 @@ abstract class RebuildFilePatches : JavaLauncherTask() {
         }
 
         git("switch", "-").executeSilently(silenceErr = true)
-        if (filesWithNewAts.isNotEmpty()) {
-            try {
-                // we need to rebase, so that the new file commit is part of the tree again.
-                // for that we use GIT_SEQUENCE_EDITOR to drop the first commit
-                // and then execs for all the files that remove the papter
-                // todo detect if sed is not present (windows) and switch out sed for something else
-                @Language("Shell Script")
-                val sequenceEditor = "sed -i -e 0,/pick/{s/pick/drop/}"
-                val execs = filesWithNewAts
-                    .map { "sed -i -e 's|// Paper-AT:.*||g' $it && ((git add $it && git commit --amend --no-edit) || true)" }
-                    .flatMap { listOf("--exec", it) }.toTypedArray()
-                git.withEnv(
-                    mapOf("GIT_SEQUENCE_EDITOR" to sequenceEditor)
-                )("rebase", "-i", "file", "--strategy-option=theirs", *execs).executeSilently()
-            } catch (e: Exception) {
-                // TODO better message to inform the user on what to do
-                throw RuntimeException("Encountered conflicts while rebuilding file patches.", e)
-            }
-        }
         git("stash", "pop").runSilently(silenceErr = true)
 
         val patchDirGit = Git(patchDir)
-        patchDirGit("add", "-A", ".").executeSilently()
+        patchDirGit("add", "-A", ".").executeSilently(silenceErr = true)
 
         logger.lifecycle("Rebuilt $result patches")
     }
@@ -202,103 +146,4 @@ abstract class RebuildFilePatches : JavaLauncherTask() {
             .operate()
         return result.summary.changedFiles
     }
-
-    private fun handleAts(
-        baseDir: Path,
-        inputDir: Path,
-        atFile: RegularFileProperty,
-        atFileOut: RegularFileProperty,
-    ): MutableList<String> {
-        val oldAts = if (atFile.isPresent) {
-            AccessTransformFormats.FML.read(atFile.path)
-        } else {
-            AccessTransformSet.create()
-        }
-
-        // handle AT
-        val filesWithNewAts = mutableListOf<String>()
-        baseDir.walk()
-            .map { it.relativeTo(baseDir).invariantSeparatorsPathString }
-            .filter { it.endsWith(".java") }
-            .forEach {
-                val ats = AccessTransformSet.create()
-                val source = inputDir.resolve(it)
-                val decomp = baseDir.resolve(it)
-                val className = it.replace(".java", "")
-                if (handleATInSource(source, ats, className)) {
-                    handleATInBase(decomp, ats)
-                    filesWithNewAts.add(it)
-                }
-                oldAts.merge(ats)
-            }
-
-        if (atFileOut.isPresent) {
-            AccessTransformFormats.FML.writeLF(
-                atFileOut.path,
-                oldAts,
-                "# This file is auto generated, any changes may be overridden!\n# See CONTRIBUTING.md on how to add access transformers."
-            )
-        }
-
-        return filesWithNewAts
-    }
-
-    private fun handleATInBase(decomp: Path, newAts: AccessTransformSet) {
-        if (newAts.classes.isEmpty()) {
-            return
-        }
-
-        val at = temporaryDir.toPath().resolve("ats.cfg").createParentDirectories()
-        AccessTransformFormats.FML.writeLF(at, newAts)
-        println("OLD: " + decomp.readText())
-        ats.run(
-            launcher.get(),
-            decomp,
-            decomp,
-            at,
-            temporaryDir.toPath().resolve("jst_work"),
-            singleFile = true,
-        )
-        println("NEW: " + decomp.readText())
-    }
-
-    private fun handleATInSource(source: Path, newAts: AccessTransformSet, className: String): Boolean {
-        val sourceLines = source.readLines()
-        var foundNew = false
-        val fixedLines = ArrayList<String>(sourceLines.size)
-        sourceLines.forEach { line ->
-            if (!line.contains("// Paper-AT: ")) {
-                fixedLines.add(line)
-                return@forEach
-            }
-
-            foundNew = true
-
-            val split = line.split("// Paper-AT: ")
-            val at = split[1]
-            try {
-                val atClass = newAts.getOrCreateClass(className)
-                val parts = at.split(" ")
-                val accessTransform = atFromString(parts[0])
-                val name = parts[1]
-                val index = name.indexOf('(')
-                if (index == -1) {
-                    atClass.mergeField(name, accessTransform)
-                } else {
-                    atClass.mergeMethod(MethodSignature.of(name.substring(0, index), name.substring(index)), accessTransform)
-                }
-                logger.lifecycle("Found new AT in $className: $at -> $accessTransform")
-            } catch (ex: Exception) {
-                throw PaperweightException("Found invalid AT '$at' in class $className")
-            }
-
-            fixedLines.add(split[0])
-        }
-
-        if (foundNew) {
-            source.writeText(fixedLines.joinToString("\n", postfix = "\n"), Charsets.UTF_8)
-        }
-
-        return foundNew
-    }
 }
diff --git a/paperweight-core/src/test/kotlin/io/papermc/paperweight/FunctionalTest.kt b/paperweight-core/src/test/kotlin/io/papermc/paperweight/FunctionalTest.kt
index 936982aaf..6f77ad8e2 100644
--- a/paperweight-core/src/test/kotlin/io/papermc/paperweight/FunctionalTest.kt
+++ b/paperweight-core/src/test/kotlin/io/papermc/paperweight/FunctionalTest.kt
@@ -23,6 +23,7 @@
 package io.papermc.paperweight
 
 import io.papermc.paperweight.util.*
+import io.papermc.paperweight.util.constants.*
 import java.net.URL
 import java.nio.file.Path
 import java.nio.file.Paths
@@ -42,7 +43,7 @@ class FunctionalTest {
 
     val debug = true
 
-    @Disabled
+    @Disabled("only used for debugging")
     @Test
     fun setupCleanTestRepo() {
         val projectDir = Path.of("F:\\Projects\\paperweight\\test").cleanFile().createDirectories()
@@ -90,34 +91,6 @@ class FunctionalTest {
             tempDir.resolve("fake-patches/sources/Test.java.patch").readText()
         )
 
-        // add AT to source -> patch and AT file is updated
-        println("adding at to source")
-        modifyFile(tempDir.resolve("test-server/src/minecraft/java/Test.java")) {
-            it.replace(
-                "\"2\";",
-                "\"2\"; // Woo"
-            ).replace("public final String getTest2() {", "public String getTest2() {// Paper-AT: public-f getTest2()Ljava/lang/String;")
-        }
-
-        Git(tempDir.resolve("test-server/src/minecraft/java")).let { git ->
-            git("add", ".").executeSilently()
-            git("commit", "--fixup", "file").executeSilently()
-            git("rebase", "--autosquash", "upstream/main").executeSilently()
-        }
-
-        println("\nrunning rebuildPatches again\n")
-        val rebP2 = gradleRunner
-            .withArguments("rebuildPatches", "--stacktrace", "-Dfake=true")
-            .withDebug(debug)
-            .build()
-
-        assertEquals(rebP2.task(":test-server:rebuildPatches")?.outcome, TaskOutcome.SUCCESS)
-        assertEquals(
-            testResource.resolve("fake-patches/expected/Test.java.patch").readText(),
-            tempDir.resolve("fake-patches/sources/Test.java.patch").readText()
-        )
-        assertEquals(testResource.resolve("build-data/expected.at").readText(), tempDir.resolve("build-data/fake.at").readText())
-
         // feature patch
         println("\nmodifying feature patch\n")
         modifyFile(tempDir.resolve("test-server/src/minecraft/java/Test.java")) {
diff --git a/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/tasks/patching/ProcessNewSourceATsTest.kt b/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/tasks/patching/ProcessNewSourceATsTest.kt
new file mode 100644
index 000000000..c5a064c01
--- /dev/null
+++ b/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/tasks/patching/ProcessNewSourceATsTest.kt
@@ -0,0 +1,70 @@
+/*
+ * paperweight is a Gradle plugin for the PaperMC project.
+ *
+ * Copyright (c) 2023 Kyle Wood (DenWav)
+ *                    Contributors
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation;
+ * version 2.1 only, no later versions.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
+ * USA
+ */
+
+package io.papermc.paperweight.core.tasks.patching
+
+import io.papermc.paperweight.tasks.TaskTest
+import io.papermc.paperweight.util.constants.MACHE_TAG_ATS
+import java.nio.file.Path
+import org.gradle.kotlin.dsl.register
+import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Disabled
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.io.TempDir
+
+class ProcessNewSourceATsTest : TaskTest() {
+    private lateinit var task: ProcessNewSourceATs
+
+    @BeforeEach
+    fun setup() {
+        val project = setupProject()
+        project.plugins.apply("java")
+        task = project.tasks.register("processNewSourceATs", ProcessNewSourceATs::class).get()
+    }
+
+    @Test
+    @Disabled("need to set jst")
+    fun `should process source access transformers`(@TempDir tempDir: Path) {
+        val testResource = Path.of("src/test/resources/process_new_source_ats")
+        val testInput = testResource.resolve("input")
+
+        val source = setupDir(tempDir, testInput, "source").toFile()
+        setupGitRepo(source, "main", MACHE_TAG_ATS)
+        setupGitRepo(tempDir.toFile(), "main", "dum")
+        setupGitHook(source)
+        val base = setupDir(tempDir, testInput, "base").toFile()
+        val atFile = testInput.resolve("ats.at").toFile()
+
+        task.base.set(base)
+        task.input.set(source)
+        task.atFile.set(atFile)
+
+        task.ats.jst.setFrom() // TODO fix
+
+        task.run()
+
+        val testOutput = testResource.resolve("output")
+        compareDir(tempDir, testOutput, "base")
+        compareDir(tempDir, testOutput, "source")
+        compareFile(tempDir, testOutput, "ats.at")
+    }
+}
diff --git a/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatchesTest.kt b/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatchesTest.kt
index dcc491c59..0bbb41c7f 100644
--- a/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatchesTest.kt
+++ b/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/tasks/patching/RebuildFilePatchesTest.kt
@@ -23,11 +23,11 @@
 package io.papermc.paperweight.core.tasks.patching
 
 import io.papermc.paperweight.tasks.*
+import io.papermc.paperweight.util.constants.*
 import java.nio.file.Path
 import kotlin.test.BeforeTest
 import kotlin.test.Test
 import org.gradle.kotlin.dsl.*
-import org.junit.jupiter.api.Disabled
 import org.junit.jupiter.api.io.CleanupMode
 import org.junit.jupiter.api.io.TempDir
 
@@ -41,8 +41,6 @@ class RebuildFilePatchesTest : TaskTest() {
         task = project.tasks.register("rebuildPatches", RebuildFilePatches::class).get()
     }
 
-    // TODO
-    @Disabled("worker api not available here")
     @Test
     fun `should rebuild patches`(@TempDir(cleanup = CleanupMode.ON_SUCCESS) tempDir: Path) {
         println("running in $tempDir")
@@ -50,19 +48,15 @@ class RebuildFilePatchesTest : TaskTest() {
         val testInput = testResource.resolve("input")
 
         val source = setupDir(tempDir, testInput, "source").toFile()
-        setupGitRepo(source, "main", "file")
+        setupGitRepo(source, "main", MACHE_TAG_FILE)
         setupGitRepo(tempDir.toFile(), "main", "dum")
         setupGitHook(source)
         val base = setupDir(tempDir, testInput, "base").toFile()
         val patches = tempDir.resolve("patches").toFile()
-        val atFile = testInput.resolve("ats.at").toFile()
-        val atFileOut = tempDir.resolve("ats.at").toFile()
 
         task.input.set(source)
         task.base.set(base)
         task.patches.set(patches)
-        task.atFile.set(atFile)
-        task.atFileOut.set(atFileOut)
         task.verbose.set(true)
 
         task.run()
@@ -71,6 +65,5 @@ class RebuildFilePatchesTest : TaskTest() {
         compareDir(tempDir, testOutput, "base")
         compareDir(tempDir, testOutput, "source")
         compareDir(tempDir, testOutput, "patches")
-        compareFile(tempDir, testOutput, "ats.at")
     }
 }
diff --git a/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/util/ApplySourceATsTest.kt b/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/util/ApplySourceATsTest.kt
deleted file mode 100644
index d42a662dd..000000000
--- a/paperweight-core/src/test/kotlin/io/papermc/paperweight/core/util/ApplySourceATsTest.kt
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * paperweight is a Gradle plugin for the PaperMC project.
- *
- * Copyright (c) 2023 Kyle Wood (DenWav)
- *                    Contributors
- *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation;
- * version 2.1 only, no later versions.
- *
- * This library is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this library; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301
- * USA
- */
-
-package io.papermc.paperweight.core.util
-
-import io.papermc.paperweight.tasks.*
-
-class ApplySourceATsTest : TaskTest() {
-    /* TODO: re-add a test for this
-    private lateinit var task: ApplySourceAT
-
-    private val workerExecutor: WorkerExecutor = mockk()
-    private val workQueue: WorkQueue = mockk()
-
-    @BeforeTest
-    fun setup() {
-        val project = setupProject()
-        task = project.tasks.register("applySourceAT", ApplySourceAT::class).get()
-        mockkObject(task)
-
-        every { task.worker } returns workerExecutor
-        every { workerExecutor.processIsolation(any()) } returns workQueue
-        every { workQueue.submit(ApplySourceATWorker::class, any()) } answers {
-            val action = object : ApplySourceATWorker() {
-                override fun getParameters(): Params {
-                    return mockk<Params>().also {
-                        every { it.inputJar.get() } returns task.inputJar.get()
-                        every { it.atFile.get() } returns task.atFile.get()
-                        every { it.outputJar.get() } returns task.outputJar.get()
-                        every { it.minecraftClasspath } returns task.minecraftClasspath
-                    }
-                }
-            }
-            action.execute()
-        }
-    }
-
-    @Test
-    fun `should apply source access transformers`(@TempDir tempDir: Path) {
-        val testResource = Path.of("src/test/resources/apply_source_at")
-        val testInput = testResource.resolve("input")
-
-        val inputJar = createZip(tempDir, testInput, "Test.jar", "Test.java", "Unrelated.java")
-        val atFile = testInput.resolve("ats.at").toFile()
-        val outputJar = tempDir.resolve("output.jar")
-
-        task.inputJar.set(inputJar.toFile())
-        task.atFile.set(atFile)
-        task.outputJar.set(outputJar.toFile())
-
-        task.run()
-
-        val testOutput = testResource.resolve("output")
-        val expectedJar = createZip(tempDir, testOutput, "expected.jar", "Test.java", "Unrelated.java")
-        compareZip(outputJar, expectedJar)
-    }
-     */
-}
diff --git a/paperweight-core/src/test/resources/functional_test/fake-patches/expected/0001-Feature.patch b/paperweight-core/src/test/resources/functional_test/fake-patches/expected/0001-Feature.patch
index 7d91209a3..b9b8c1de0 100644
--- a/paperweight-core/src/test/resources/functional_test/fake-patches/expected/0001-Feature.patch
+++ b/paperweight-core/src/test/resources/functional_test/fake-patches/expected/0001-Feature.patch
@@ -5,12 +5,12 @@ Subject: [PATCH] Feature
 
 
 diff --git a/Test.java b/Test.java
-index 51f6794c111f68e72cc4054c01f0c8896afaf292..d047a159f76d162bc24b030a575252202e57080c 100644
+index bf731c042bf7f59b60378df1d61302e1769a6a77..13e57904b05e4b98b8b105511254c2f6c1b1924d 100644
 --- a/Test.java
 +++ b/Test.java
 @@ -13,4 +13,8 @@ public class Test {
-     public String getTest2() {
-         return this.test + "2"; // Woo
+     public final String getTest2() {
+         return this.test + "2";
      }
 +
 +    public String feature() {
diff --git a/paperweight-lib/src/test/resources/rebuild_patches/input/ats.at b/paperweight-core/src/test/resources/process_new_source_ats/input/ats.at
similarity index 88%
rename from paperweight-lib/src/test/resources/rebuild_patches/input/ats.at
rename to paperweight-core/src/test/resources/process_new_source_ats/input/ats.at
index c46fe9b71..8130cbdcf 100644
--- a/paperweight-lib/src/test/resources/rebuild_patches/input/ats.at
+++ b/paperweight-core/src/test/resources/process_new_source_ats/input/ats.at
@@ -1,3 +1,3 @@
 # This file is auto generated, any changes may be overridden!
 # See CONTRIBUTING.md on how to add access transformers.
-public Test dum
+
diff --git a/paperweight-lib/src/test/resources/rebuild_patches/output/base/Test.java b/paperweight-core/src/test/resources/process_new_source_ats/input/base/Test.java
similarity index 84%
rename from paperweight-lib/src/test/resources/rebuild_patches/output/base/Test.java
rename to paperweight-core/src/test/resources/process_new_source_ats/input/base/Test.java
index fd852a162..671b5f49e 100644
--- a/paperweight-lib/src/test/resources/rebuild_patches/output/base/Test.java
+++ b/paperweight-core/src/test/resources/process_new_source_ats/input/base/Test.java
@@ -1,7 +1,7 @@
 public class Test {
 
     public int dum;
-    public String test;
+    private final String test;
 
     public Test(String test) {
         this.test = test;
diff --git a/paperweight-lib/src/test/resources/apply_source_at/input/Unrelated.java b/paperweight-core/src/test/resources/process_new_source_ats/input/base/Unrelated.java
similarity index 100%
rename from paperweight-lib/src/test/resources/apply_source_at/input/Unrelated.java
rename to paperweight-core/src/test/resources/process_new_source_ats/input/base/Unrelated.java
diff --git a/paperweight-core/src/test/resources/process_new_source_ats/input/source/Test.java b/paperweight-core/src/test/resources/process_new_source_ats/input/source/Test.java
new file mode 100644
index 000000000..ac6fad0a9
--- /dev/null
+++ b/paperweight-core/src/test/resources/process_new_source_ats/input/source/Test.java
@@ -0,0 +1,13 @@
+public class Test {
+
+    public int dum;
+    private final String test;
+
+    public Test(String test) {
+        this.test = test;
+    }
+
+    public String getTest() {// Paper-AT: public-f getTest()Ljava/lang/String;
+        return test;
+    }
+}
diff --git a/paperweight-lib/src/test/resources/apply_source_at/output/Unrelated.java b/paperweight-core/src/test/resources/process_new_source_ats/input/source/Unrelated.java
similarity index 100%
rename from paperweight-lib/src/test/resources/apply_source_at/output/Unrelated.java
rename to paperweight-core/src/test/resources/process_new_source_ats/input/source/Unrelated.java
diff --git a/paperweight-lib/src/test/resources/rebuild_patches/output/ats.at b/paperweight-core/src/test/resources/process_new_source_ats/output/ats.at
similarity index 60%
rename from paperweight-lib/src/test/resources/rebuild_patches/output/ats.at
rename to paperweight-core/src/test/resources/process_new_source_ats/output/ats.at
index 3b4280360..0c17e0099 100644
--- a/paperweight-lib/src/test/resources/rebuild_patches/output/ats.at
+++ b/paperweight-core/src/test/resources/process_new_source_ats/output/ats.at
@@ -1,5 +1,3 @@
 # This file is auto generated, any changes may be overridden!
 # See CONTRIBUTING.md on how to add access transformers.
-private+f Test getTest()Ljava/lang/String;
-public Test dum
-public-f Test test
+public-f Test getTest()Ljava/lang/String;
diff --git a/paperweight-lib/src/test/resources/apply_source_at/output/Test.java b/paperweight-core/src/test/resources/process_new_source_ats/output/source/Test.java
similarity index 81%
rename from paperweight-lib/src/test/resources/apply_source_at/output/Test.java
rename to paperweight-core/src/test/resources/process_new_source_ats/output/source/Test.java
index 869744fb8..a761c51b1 100644
--- a/paperweight-lib/src/test/resources/apply_source_at/output/Test.java
+++ b/paperweight-core/src/test/resources/process_new_source_ats/output/source/Test.java
@@ -7,7 +7,7 @@ public Test(String test) {
         this.test = test;
     }
 
-    private final String getTest() {
+    public String getTest() {
         return test;
     }
 }
diff --git a/paperweight-core/src/test/resources/process_new_source_ats/output/source/Unrelated.java b/paperweight-core/src/test/resources/process_new_source_ats/output/source/Unrelated.java
new file mode 100644
index 000000000..c821a33ff
--- /dev/null
+++ b/paperweight-core/src/test/resources/process_new_source_ats/output/source/Unrelated.java
@@ -0,0 +1,3 @@
+class Unrealted {
+
+}
diff --git a/paperweight-lib/src/test/resources/apply_source_at/input/Test.java b/paperweight-core/src/test/resources/rebuild_patches/input/base/Test.java
similarity index 100%
rename from paperweight-lib/src/test/resources/apply_source_at/input/Test.java
rename to paperweight-core/src/test/resources/rebuild_patches/input/base/Test.java
diff --git a/paperweight-lib/src/test/resources/rebuild_patches/output/source/Test.java b/paperweight-core/src/test/resources/rebuild_patches/input/source/Test.java
similarity index 71%
rename from paperweight-lib/src/test/resources/rebuild_patches/output/source/Test.java
rename to paperweight-core/src/test/resources/rebuild_patches/input/source/Test.java
index a2d35e435..bb72c175b 100644
--- a/paperweight-lib/src/test/resources/rebuild_patches/output/source/Test.java
+++ b/paperweight-core/src/test/resources/rebuild_patches/input/source/Test.java
@@ -1,13 +1,13 @@
 public class Test {
 
     public int dum;
-    public String test;
+    private final String test;
 
     public Test(String test) {
         this.test = test;
     }
 
-    private final String getTest() {
+    public String getTest() {
         return test + "Test"; // Test
     }
 }
diff --git a/paperweight-lib/src/test/resources/rebuild_patches/input/base/Test.java b/paperweight-core/src/test/resources/rebuild_patches/output/base/Test.java
similarity index 100%
rename from paperweight-lib/src/test/resources/rebuild_patches/input/base/Test.java
rename to paperweight-core/src/test/resources/rebuild_patches/output/base/Test.java
diff --git a/paperweight-lib/src/test/resources/rebuild_patches/output/patches/Test.java.patch b/paperweight-core/src/test/resources/rebuild_patches/output/patches/Test.java.patch
similarity index 77%
rename from paperweight-lib/src/test/resources/rebuild_patches/output/patches/Test.java.patch
rename to paperweight-core/src/test/resources/rebuild_patches/output/patches/Test.java.patch
index aaa46dd44..58d2f2fdb 100644
--- a/paperweight-lib/src/test/resources/rebuild_patches/output/patches/Test.java.patch
+++ b/paperweight-core/src/test/resources/rebuild_patches/output/patches/Test.java.patch
@@ -3,7 +3,7 @@
 @@ -8,6 +_,6 @@
      }
  
-     private final String getTest() {
+     public String getTest() {
 -        return test;
 +        return test + "Test"; // Test
      }
diff --git a/paperweight-lib/src/test/resources/rebuild_patches/input/source/Test.java b/paperweight-core/src/test/resources/rebuild_patches/output/source/Test.java
similarity index 52%
rename from paperweight-lib/src/test/resources/rebuild_patches/input/source/Test.java
rename to paperweight-core/src/test/resources/rebuild_patches/output/source/Test.java
index 1e61ad8fc..bb72c175b 100644
--- a/paperweight-lib/src/test/resources/rebuild_patches/input/source/Test.java
+++ b/paperweight-core/src/test/resources/rebuild_patches/output/source/Test.java
@@ -1,13 +1,13 @@
 public class Test {
 
     public int dum;
-    public String test;// Paper-AT: public-f test
+    private final String test;
 
     public Test(String test) {
         this.test = test;
     }
 
-    private final String getTest() {// Paper-AT: private+f getTest()Ljava/lang/String;
+    public String getTest() {
         return test + "Test"; // Test
     }
 }
diff --git a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/util/constants/constants.kt b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/util/constants/constants.kt
index a35d44da8..ed864814a 100644
--- a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/util/constants/constants.kt
+++ b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/util/constants/constants.kt
@@ -26,7 +26,7 @@ import org.gradle.api.Task
 
 const val PAPERWEIGHT_EXTENSION = "paperweight"
 const val PAPERWEIGHT_DEBUG = "paperweight.debug"
-fun paperweightDebug(): Boolean = System.getProperty(PAPERWEIGHT_DEBUG, "false") == "true"
+fun paperweightDebug(): Boolean = true
 const val PAPERWEIGHT_VERBOSE_APPLY_PATCHES = "paperweight.verboseApplyPatches"
 
 const val MC_LIBRARY_URL = "https://libraries.minecraft.net/"
@@ -117,6 +117,14 @@ const val DOWNLOAD_SERVICE_NAME = "paperweightDownloadService"
 private const val MACHE_PATH = "$PAPER_PATH/mache"
 const val BASE_PROJECT = "$MACHE_PATH/base"
 
+// when changing these, also change it in the post-rewrite.sh!
+const val MACHE_TAG_ROOT = "ROOT"
+const val MACHE_TAG_VANILLA = "Vanilla"
+const val MACHE_TAG_PATCHES = "Mache"
+const val MACHE_TAG_ATS = "ATs"
+const val MACHE_TAG_IMPORTS = "Imports"
+const val MACHE_TAG_FILE = "file"
+
 fun Task.paperTaskOutput(ext: String? = null) = paperTaskOutput(name, ext)
 fun paperTaskOutput(name: String, ext: String? = null) = "$TASK_CACHE/$name" + (ext?.let { ".$it" } ?: "")
 
diff --git a/paperweight-lib/src/main/resources/post-rewrite.sh b/paperweight-lib/src/main/resources/post-rewrite.sh
index 8918da877..963ba0a27 100644
--- a/paperweight-lib/src/main/resources/post-rewrite.sh
+++ b/paperweight-lib/src/main/resources/post-rewrite.sh
@@ -1,11 +1,28 @@
-#!/bin/sh
-input=$(cat)                             # <old-object> SP <new-object> [SP <extra-info>] LF
-fileCommit=$(git rev-list -n 1 file)     # current commit tagged as "file"
-oldObject=$(echo $input | cut -d' ' -f1) # <old-object>
-newObject=$(echo $input | cut -d' ' -f2) # <new-object>
-
-if [ $oldObject = $fileCommit ]; then
-    git tag -d file > /dev/null          # delete old tag (silent)
-    git tag file "$newObject" --no-sign
-    echo "Updated tag 'file' from $oldObject to $newObject"
-fi
+#!/bin/bash
+tags=("ATs" "Imports" "file")
+declare -A tagCommits
+
+# get the current commit for each tag
+for tag in "${tags[@]}"; do
+    tagCommits["$tag"]=$(git rev-list -n 1 "$tag")
+done
+
+while IFS= read -r line; do
+    # <old-object> SP <new-object> [SP <extra-info>] LF
+    oldObject=$(echo "$line" | cut -d' ' -f1)
+    newObject=$(echo "$line" | cut -d' ' -f2)
+
+    for tag in "${tags[@]}"; do
+        if [ "$oldObject" = "${tagCommits[$tag]}" ]; then
+            # delete old tag (silent) and add new tag
+            git tag -d "$tag" > /dev/null
+            git tag "$tag" "$newObject" --no-sign
+            echo "Updated tag '$tag' from $oldObject to $newObject"
+        fi
+    done
+
+    # if we have updated the file tag, we can stop, no tags after that
+    if [ "$oldObject" = "${tagCommits["file"]}" ] || [ "$newObject" = "${tagCommits["file"]}" ]; then
+        break
+    fi
+done
diff --git a/paperweight-lib/src/test/resources/apply_source_at/input/ats.at b/paperweight-lib/src/test/resources/apply_source_at/input/ats.at
deleted file mode 100644
index 693b10bf2..000000000
--- a/paperweight-lib/src/test/resources/apply_source_at/input/ats.at
+++ /dev/null
@@ -1,5 +0,0 @@
-# This file is auto generated, any changes may be overridden!
-# See CONTRIBUTING.md on how to add access transformers.
-public-f Test test
-public+f Test dum
-private+f Test getTest()Ljava/lang/String;