diff --git a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/FixupFilePatches.kt b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/FixupFilePatches.kt
index 03c85b5e..16ed771d 100644
--- a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/FixupFilePatches.kt
+++ b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/FixupFilePatches.kt
@@ -38,6 +38,7 @@ abstract class FixupFilePatches : BaseTask() {
     @TaskAction
     fun run() {
         val git = Git(repo)
+        git("commit", "add", ".").executeOut()
         git("commit", "--fixup", "file").executeOut()
         git("-c", "sequence.editor=:", "rebase", "-i", "--autosquash", "mache/main").executeOut()
     }
diff --git a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/SetupPaperScript.kt b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/SetupPaperScript.kt
index beca3de5..c3f2448c 100644
--- a/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/SetupPaperScript.kt
+++ b/paperweight-lib/src/main/kotlin/io/papermc/paperweight/tasks/softspoon/SetupPaperScript.kt
@@ -72,6 +72,7 @@ abstract class SetupPaperScript : BaseTask() {
                 "Puts the current source changes into the file patches commit",
                 listOf(
                     "cd %root%/paper-server/src/vanilla/java",
+                    "git add .",
                     "git commit --fixup file",
                     "git -c sequence.editor=: rebase -i --autosquash mache/main"
                 )
@@ -82,6 +83,7 @@ abstract class SetupPaperScript : BaseTask() {
                 "Puts the current resource changes into the file patches commit",
                 listOf(
                     "cd %root%/paper-server/src/vanilla/resources",
+                    "git add .",
                     "git commit --fixup file",
                     "git -c sequence.editor=: rebase -i --autosquash mache/main"
                 )