How to include R.java in a custom android build?

Question

I'm trying to add an application to a custom android build, but it is unable to understand resources like Theme.AppCompat.Light.DarkActionBar and colorPrimary and colorAccent, which leads me to believe it is having trouble reading and building R.java.

My Error

target R.java/Manifest.java: MyApplication21 (out/target/common/obj/APPS/MyApplication21_intermediates/src/R.stamp)
packages/apps/MyApplication21/res/values/styles.xml:4: error: Error retrieving parent for item: No resource found that matches the given name 'Theme.AppCompat.Light.DarkActionBar'.

packages/apps/MyApplication21/res/values/styles.xml:8: error: Error: No resource found that matches the given name: attr 'colorAccent'.

packages/apps/MyApplication21/res/values/styles.xml:6: error: Error: No resource found that matches the given name: attr 'colorPrimary'.

packages/apps/MyApplication21/res/values/styles.xml:7: error: Error: No resource found that matches the given name: attr 'colorPrimaryDark'.

build/core/package_internal.mk:236: recipe for target 'out/target/common/obj/APPS/MyApplication21_intermediates/src/R.stamp' failed
make: *** [out/target/common/obj/APPS/MyApplication21_intermediates/src/R.stamp] Error 1
make: Leaving directory '/home/mkemp/android'

#### make failed to build some targets  ####

What I did:

1. Created an android app. This app compiles in android studio.
2. Copied the manifest, java (renamed src), and res directories into my custom build: android/packages/apps/MyApplication21

3. Created an Android.mk file

   LOCAL_PATH:= $(call my-dir)
   include $(CLEAR_VARS)
   
   LOCAL_MODULE_TAGS := optional
   
   # Java sources are in src
   LOCAL_SRC_FILES := $(call all-java-files-under, src)
   
   # Resources are in res
   LOCAL_RESOURCE_DIR := $(LOCAL_PATH)/res
   
   # These jars are needed
   LOCAL_STATIC_JAVA_LIBRARIES += android-support-v7-appcompat \
   android-support-v4 
   
   # The name of this application
   LOCAL_PACKAGE_NAME := MyApplication21
   
   # No proguard
   LOCAL_PROGUARD_ENABLED := disabled
   

So far I have resolved errors that include not being able to understand Java classes like ActionBarActivity and TaskStackBuilder by including android-support-v7-appcompat and android-support-v4 in that order, into the Android.mk file, but I have no idea what Java library I should call in order to generate an R.java file.

Can anyone help?

Edit:

I notice that an R.stamp file is not being created in android/out/target/common/obj/APPS/MyApplication21/src, which should be built there judging by the other apps in the APPS folder ... and again leads me to believe the culprit is the R.java file not being generated correctly.