fix: broken control flow of `includeFilter`

src/main/kotlin/app/revanced/cli/command/MainCommand.kt

@@ -63,9 +63,6 @@ internal object MainCommand : Runnable {
     )
     var clean: Boolean = false
 
-    @Option(names = ["--sign"], description = ["Sign the apk file"])
-    var signApk: Boolean = false
-
     override fun run() {
         if (listOnly) {
             for (patchBundlePath in patchBundles) for (patch in JarPatchBundle(patchBundlePath).loadPatches()) {
@@ -82,11 +79,11 @@ internal object MainCommand : Runnable {
             Adb(outputFile, patcher.data.packageMetadata.packageName, deploy!!, install)
         }
 
-        val patchedFile = if (signApk) File(cacheDirectory).resolve("raw.apk") else outputFile
+        val patchedFile = if (install) File(cacheDirectory).resolve("raw.apk") else outputFile
 
         Patcher.start(patcher, patchedFile)
 
-        if (signApk) {
+        if (install) {
             Signing.start(
                 patchedFile,
                 outputFile,

src/main/kotlin/app/revanced/utils/patcher/Patcher.kt

@@ -6,7 +6,7 @@ import app.revanced.cli.command.MainCommand.patchBundles
 import app.revanced.patcher.Patcher
 import app.revanced.patcher.data.base.Data
 import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
-import app.revanced.patcher.extensions.PatchExtensions.excludeByDefault
+import app.revanced.patcher.extensions.PatchExtensions.include
 import app.revanced.patcher.extensions.PatchExtensions.patchName
 import app.revanced.patcher.patch.base.Patch
 import app.revanced.patcher.util.patch.implementation.JarPatchBundle
@@ -25,8 +25,13 @@ fun Patcher.addPatchesFiltered(
 
             val prefix = "[skipped] $patchName"
 
-            if ((includeFilter && !MainCommand.includedPatches.contains(patchName)) || patch.excludeByDefault) {
-                println(prefix)
+            if (includeFilter) {
+                if (!MainCommand.includedPatches.contains(patchName)) {
+                    println("$prefix: Explicitly excluded.")
+                    return@patch
+                }
+            } else if (!patch.include) {
+                println("$prefix: Implicitly excluded.")
                 return@patch
             }