Git Merge - Brave New World

I already have a backup and did merging the "old school" way - but now I'm trying to do it the git way !
We have 3 branches master API (mine) WebGUI (MaVo's) and I'm trying to merge MaVo's WebGUI branch into mine. I made a pull request and was pleasantly surpised to the auto-merge and views of the changes (well done Git & GitHub).. I was excited that only 3 files were in conflict. I know the changes at the moment I want to keep all the changes on my branch which include 2 modified files & 1 delete

This is were I am in the process :

C:\>cd mrl\myrobotlab

C:\mrl\myrobotlab>git fetch origin

C:\mrl\myrobotlab>git checkout -b WebGUI origin/WebGUI

Unlink of file 'build-lib/tools.jar' failed. Should I try again? (y/n) y

Checking out files: 100% (183/183), done.

M src/org/myrobotlab/kinematics/DHLink.java

M src/resource/Arduino/MRLComm.ino

Branch WebGUI set up to track remote branch WebGUI from origin.

Switched to a new branch 'WebGUI'

C:\mrl\myrobotlab>git merge API

Auto-merging src/resource/WebGUI/js/app.js

CONFLICT (add/add): Merge conflict in src/resource/WebGUI/js/app.js

Auto-merging src/resource/WebGUI/index.html

CONFLICT (add/add): Merge conflict in src/resource/WebGUI/index.html

Removing src/org/myrobotlab/webgui/WSServer.java

Removing src/org/myrobotlab/webgui/SOAPProcessor.java

Removing src/org/myrobotlab/webgui/ReturnType.java

Removing src/org/myrobotlab/webgui/ResourceProcessor.java

Removing src/org/myrobotlab/webgui/RESTProcessor.java

Removing src/org/myrobotlab/webgui/REST.java

Removing src/org/myrobotlab/service/interfaces/HTTPProcessor.java

CONFLICT (modify/delete): src/org/myrobotlab/service/WebGUI2.java deleted in API and modified in HEAD. Version HEAD of s

rc/org/myrobotlab/service/WebGUI2.java left in tree.

Removing src/org/myrobotlab/service/SpeechRecognitionGoogle.java

Removing src/org/myrobotlab/service/SpeakerRecognition.java

Removing src/org/myrobotlab/service/Cortex.java

Removing src/org/myrobotlab/net/http/ResponseException.java

Removing src/org/myrobotlab/net/http/Response.java

Removing src/org/myrobotlab/framework/MessageFormatter.java

Removing src/org/myrobotlab/framework/MRLError.java

Removing src/org/myrobotlab/framework/Errors.java

Removing src/org/myrobotlab/control/CortexGUI.java

Auto-merging src/org/myrobotlab/codec/serial/HexCodec.java

Auto-merging src/org/myrobotlab/codec/serial/DecimalCodec.java

Auto-merging src/org/myrobotlab/codec/serial/CodecOutputStream.java

Auto-merging src/org/myrobotlab/codec/serial/AsciiCodec.java

Auto-merging src/org/myrobotlab/codec/serial/ArduinoMsgCodec.java

Auto-merging src/org/myrobotlab/codec/serial/ArduinoBindingsGenerator.java

Auto-merging src/org/myrobotlab/codec/Encoder.java

Removing docs/multiParameter.dia

Removing docs/kinect.png

Removing docs/attach.dia

Automatic merge failed; fix conflicts and then commit the result.

C:\mrl\myrobotlab>git checkout src/resource/WebGUI/js/app.js

error: path 'src/resource/WebGUI/js/app.js' is unmerged

C:\mrl\myrobotlab>git reset src/resource/WebGUI/js/app.js

Unstaged changes after reset:

M src/org/myrobotlab/kinematics/DHLink.java

U src/org/myrobotlab/service/WebGUI2.java

M src/resource/Arduino/MRLComm.ino

U src/resource/WebGUI/index.html

M src/resource/WebGUI/js/app.js

C:\mrl\myrobotlab>git checkout src/resource/WebGUI/js/app.js

C:\mrl\myrobotlab>git reset src/resource/WebGUI/index.html

Unstaged changes after reset:

M src/org/myrobotlab/kinematics/DHLink.java

U src/org/myrobotlab/service/WebGUI2.java

M src/resource/Arduino/MRLComm.ino

M src/resource/WebGUI/index.html

C:\mrl\myrobotlab>git checkout src/resource/WebGUI/index.html

C:\mrl\myrobotlab>del src/org/myrobotlab/service/WebGUI2.java

Invalid switch - "org".

C:\mrl\myrobotlab>del src\org\myrobotlab\service\WebGUI2.java

C:\mrl\myrobotlab>git checkout API

src/org/myrobotlab/service/WebGUI2.java: needs merge

error: you need to resolve your current index first

C:\mrl\myrobotlab>git commit

U src/org/myrobotlab/service/WebGUI2.java

error: 'commit' is not possible because you have unmerged files.

hint: Fix them up in the work tree,

hint: and then use 'git add/rm <file>' as

hint: appropriate to mark resolution and make a commit,

hint: or use 'git commit -a'.

fatal: Exiting because of an unresolved conflict.

C:\mrl\myrobotlab>git rm src\org\myrobotlab\service\WebGUI2.java

src/org/myrobotlab/service/WebGUI2.java: needs merge

rm 'src/org/myrobotlab/service/WebGUI2.java'

C:\mrl\myrobotlab>git checkout API

M src/org/myrobotlab/kinematics/DHLink.java

M src/resource/Arduino/MRLComm.ino

Switched to branch 'API'

Your branch is up-to-date with 'origin/API'.

C:\mrl\myrobotlab>git merge --no-ff WebGUI

Auto-merging src/resource/WebGUI/js/app.js

CONFLICT (add/add): Merge conflict in src/resource/WebGUI/js/app.js

Auto-merging src/resource/WebGUI/index.html

CONFLICT (add/add): Merge conflict in src/resource/WebGUI/index.html

CONFLICT (modify/delete): src/org/myrobotlab/service/WebGUI2.java deleted in HEAD and modified in WebGUI. Version WebGUI

of src/org/myrobotlab/service/WebGUI2.java left in tree.

Automatic merge failed; fix conflicts and then commit the result.

C:\mrl\myrobotlab>

I think I should have committed after the git rm before switching branches. Suggestions?