Properly detect if the instance is vanilla and don't treat it as custom.

logic/minecraft/InstanceVersion.cpp

@@ -157,8 +157,11 @@ bool InstanceVersion::removeFtbPack()
 bool InstanceVersion::isVanilla()
 {
 	QDir patches(PathCombine(m_instance->instanceRoot(), "patches/"));
-	if(VersionPatches.size() >= 1)
+	for(auto patchptr: VersionPatches)
+	{
+		if(patchptr->isCustom())
 			return false;
+	}
 	if(QFile::exists(PathCombine(m_instance->instanceRoot(), "custom.json")))
 		return false;
 	if(QFile::exists(PathCombine(m_instance->instanceRoot(), "version.json")))

logic/minecraft/MinecraftVersion.cpp

@@ -155,3 +155,9 @@ bool MinecraftVersion::hasUpdate()
 {
 	return m_versionSource == Remote || (m_versionSource == Local && upstreamUpdate);
 }
+
+bool MinecraftVersion::isCustom()
+{
+	// if we add any other source types, this will evaluate to false for them.
+	return m_versionSource != Builtin && m_versionSource != Local && m_versionSource != Remote;
+}

logic/minecraft/MinecraftVersion.h

@@ -47,6 +47,7 @@ public: /* methods */
 	virtual QString getPatchFilename() override;
 	bool needsUpdate();
 	bool hasUpdate();
+	virtual bool isCustom();
 
 private: /* methods */
 	void applyFileTo(InstanceVersion *version);

logic/minecraft/VersionBuilder.cpp

@@ -199,6 +199,7 @@ void VersionBuilder::buildFromMultilayer()
 		throw VersionIncomplete("org.lwjgl");
 	}
 	lwjglPatch->setOrder(-1);
+	lwjgl->setVanilla(true);
 	m_version->VersionPatches.append(lwjglPatch);
 
 	// load all patches, put into map for ordering, apply in the right order

logic/minecraft/VersionFile.h

@@ -53,9 +53,18 @@ public: /* methods */
 	{
 		return filename;
 	}
+	virtual bool isCustom()
+	{
+		return !isVanilla;
+	};
+	void setVanilla (bool state)
+	{
+		isVanilla = state;
+	}
 
 public: /* data */
 	int order = 0;
+	bool isVanilla = false;
 	QString name;
 	QString fileId;
 	QString version;

logic/minecraft/VersionPatch.h

@@ -26,6 +26,7 @@ public:
 	virtual QString getPatchName() = 0;
 	virtual QString getPatchVersion() = 0;
 	virtual QString getPatchFilename() = 0;
+	virtual bool isCustom() = 0;
 };
 
 typedef std::shared_ptr<VersionPatch> VersionPatchPtr;