How to add .so, .mk and other native files in Android Studio?

I've to add the native files .so, .mk, .sh, .cpp in my Project in Android Studio. In eclipse .so files are added in libs folder and other files in jni and obj folder and all working fine. But in Android studio As I've added .so files in jniLibs folder and made changes in .gradle file as below

 ndk{
                abiFilters 'armeabi', 'armeabi-v7a', 'x86'
            }
sourceSets.main {
        jniLibs.srcDir 'src/main/libs' //set libs as .so's location instead of jniLibs
        jni.srcDirs = [] //disable automatic ndk-build call with auto-generated Android.mk
    }

Below is the structure of my project and the files I need to add. There are jni and obj folder that contain the native code and I've to use that.

I've seen the links available but they are outdated and nothing worked. Any help is appreciated.

Log after after doing the below changes:

sourceSets.main {
        jniLibs.srcDir 'src/main/libs' //set libs as .so's location instead of jniLibs
        jni.srcDirs = [] //disable automatic ndk-build call with auto-generated Android.mk
    }
    externalNativeBuild {
        ndkBuild {
            path 'src/main/jni/Android.mk'
        }
    }

Log:

Error while executing 'E:\Android_SDK\ndk-bundle\ndk-build.cmd' with arguments {NDK_PROJECT_PATH=null APP_BUILD_SCRIPT=E:\folder\sampleapp\app\src\main\jni\Android.mk NDK_APPLICATION_MK=E:\folder\sampleapp\app\src\main\jni\Application.mk APP_ABI=armeabi-v7a NDK_ALL_ABIS=armeabi-v7a NDK_DEBUG=1 APP_PLATFORM=android-16 NDK_OUT=E:/folder/app/build/intermediates/ndkBuild/debug/obj NDK_LIBS_OUT=E:\folder\sampleapp\app\build\intermediates\ndkBuild\debug\lib APP_SHORT_COMMANDS=false LOCAL_SHORT_COMMANDS=false -B -n}
md "E:\folder\sampleapp\app\build\intermediates\ndkBuild\debug\lib\armeabi-v7a" >NUL 2>NUL || rem
copy /b/y "E:\Android_SDK\ndk-bundle\build\\..\prebuilt\android-arm\gdbserver\gdbserver" "E:\folder\sampleapp\app\build\intermediates\ndkBuild\debug\lib\armeabi-v7a\gdbserver" > NUL
E:/Android_SDK/ndk-bundle/build//../prebuilt/windows-x86_64/bin/echo.exe [armeabi-v7a] "Gdbserver      ": "[arm-linux-androideabi] E:\folder\sampleapp\app\build\intermediates\ndkBuild\debug\lib/armeabi-v7a/gdbserver"
E:/Android_SDK/ndk-bundle/build//../prebuilt/windows-x86_64/bin/echo.exe [armeabi-v7a] "Gdbsetup       ": "E:\folder\sampleapp\app\build\intermediates\ndkBuild\debug\lib/armeabi-v7a/gdb.setup"
E:/Android_SDK/ndk-bundle/build//../prebuilt/windows-x86_64/bin/echo.exe "directory E:/Android_SDK/ndk-bundle/build//../platforms/android-16/arch-arm/usr/include E:/folder/app/src/main/jni E:/Android_SDK/ndk-bundle/build//../sources/cxx-stl/system" >> E:\folder\sampleapp\app\build\intermediates\ndkBuild\debug\lib/armeabi-v7a/gdb.setup
E:/Android_SDK/ndk-bundle/build//../prebuilt/windows-x86_64/bin/echo.exe "set solib-search-path E:/folder/app/build/intermediates/ndkBuild/debug/obj/local/armeabi-v7a" > E:\folder\sampleapp\app\build\intermediates\ndkBuild\debug\lib/armeabi-v7a/gdb.setup
process_begin: CreateProcess(NULL, "", ...) failed.
make: *** No rule to make target `E:/folder/app/src/main/jni/SerialPort.c', needed by `E:/folder/app/build/intermediates/ndkBuild/debug/obj/local/armeabi-v7a/objs-debug/serial_port/SerialPort.o'.  Stop.
Build command failed.
Error:executing external native build for ndkBuild E:\folder\sampleapp\app\src\main\jni\Android.mk
Build command failed.
Error while executing 'E:\Android_SDK\ndk-bundle\ndk-build.cmd' with arguments {NDK_PROJECT_PATH=null APP_BUILD_SCRIPT=E:\folder\sampleapp\app\src\main\jni\Android.mk NDK_APPLICATION_MK=E:\folder\sampleapp\app\src\main\jni\Application.mk APP_ABI=armeabi-v7a NDK_ALL_ABIS=armeabi-v7a NDK_DEBUG=0 APP_PLATFORM=android-16 NDK_OUT=E:/folder/app/build/intermediates/ndkBuild/release/obj NDK_LIBS_OUT=E:\folder\sampleapp\app\build\intermediates\ndkBuild\release\lib APP_SHORT_COMMANDS=false LOCAL_SHORT_COMMANDS=false -B -n}
make: *** No rule to make target `E:/folder/app/src/main/jni/SerialPort.c', needed by `E:/folder/app/build/intermediates/ndkBuild/release/obj/local/armeabi-v7a/objs/serial_port/SerialPort.o'.  Stop.
process_begin: CreateProcess(NULL, "", ...) failed.
Error:executing external native build for ndkBuild E:\folder\sampleapp\app\src\main\jni\Android.mk