Procedure to merge from another repo into your QGIS GH clone:

In your original repo where you have stuff to merge. In my case my changes lived in a branch called 'sansa-branch'. I also wanted to bring my changes through as a single commit so I used the --squash option and merged my changes into a temporary branch:

git checkout master
git branch temp
git checkout temp
git merge --squash sansa-branch
git commit -m "SANSA branding and incorporate gcp tool" -a
git format-patch master --stdout > /tmp/sansa-branch.patch 
git checkout master
git branch -D temp

Ok now you have a nice patch living in /tmp/sansa-branch.patch, so we can go into our QGIS GH clone and apply it (in this case straight into master though typically you want to apply into a branch.

cd qgis-github-clone
git apply /tmp/sansa-branch.patch 

In my case the apply process produced the following output:

/tmp/sansa-branch.patch:162528: trailing whitespace.
!define RELEASE_VERSION_NUMBER "1.7.0" 
/tmp/sansa-branch.patch:162529: trailing whitespace.
!define RELEASE_VERSION_NAME "Wroclaw" 
/tmp/sansa-branch.patch:162530: trailing whitespace.
!define RELEASE_SVN_REVISION "15643" 
/tmp/sansa-branch.patch:162577: trailing whitespace.

/tmp/sansa-branch.patch:162578: trailing whitespace.
%Module qgis.analysis 0
warning: squelched 8967 whitespace errors
warning: 8972 lines add whitespace errors.

Ok so lets see that status of our repo now:

[qgis-github-clone] git status
# On branch sansa-branch
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#    modified:   .gitignore
#    modified:   CMakeLists.txt
#    modified:   images/splash/splash.png
#    modified:   images/splash/splash.xcf.bz2
#    modified:   ms-windows/Installer-Files/UnWelcomeFinishPage.bmp
#    modified:   ms-windows/Installer-Files/WelcomeFinishPage.bmp
#    modified:   ms-windows/Installer-Files/sidelogomaster.xcf.bz2
#    modified:   ms-windows/QGIS-Installer.nsi
#    modified:   ms-windows/quickpackage.sh
#    modified:   python/CMakeLists.txt
#    modified:   python/analysis/analysis.sip
#    modified:   python/plugins/CMakeLists.txt
#    modified:   src/analysis/CMakeLists.txt
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#    python/analysis/qgsautogcpmanager.sip
#    python/analysis/qgsbilinearsampler.sip
#    python/analysis/qgscrosscorrelator.sip
#    python/analysis/qgsdatasource.sip
#    python/analysis/qgselevationmodel.sip
#    python/analysis/qgserror.sip
#    python/analysis/qgserrorlist.sip
#    python/analysis/qgsgcp.sip
#    python/analysis/qgsgcpset.sip
#    python/analysis/qgsgeoreferencer.sip
#    python/analysis/qgshasher.sip
#    python/analysis/qgsimageanalyzer.sip
#    python/analysis/qgsimagechip.sip
#    python/analysis/qgsimagefilter.sip
#    python/analysis/qgsmatrix.sip
#    python/analysis/qgsorthorectificationfilter.sip
#    python/analysis/qgsprojectionmanager.sip
#    python/analysis/qgsrasterdataset.sip
#    python/analysis/qgsrpcmodel.sip
#    python/analysis/qgssalientpoint.sip
#    python/analysis/qgssampler.sip
#    python/analysis/qgssensormodel.sip
#    python/analysis/qgssqldriver.sip
#    python/analysis/qgssqlitedriver.sip
#    python/analysis/qgswavelettransform.sip
#    python/plugins/autogcp/
#    src/analysis/autogcp/
no changes added to commit (use "git add" and/or "git commit -a")

As you can see there are a bunch of untracked files, so I will just git add them:

[qgis-github-clone] git add python/analysis/*.sip
[qgis-github-clone] git add python/plugins/autogcp/
[qgis-github-clone] git add src/analysis/autogcp/
[qgis-github-clone] git status
# On branch sansa-branch
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#    modified:   python/analysis/analysis.sip
#    new file:   python/analysis/qgsautogcpmanager.sip
#    new file:   python/analysis/qgsbilinearsampler.sip
#    new file:   python/analysis/qgscrosscorrelator.sip
#    new file:   python/analysis/qgsdatasource.sip
#    new file:   python/analysis/qgselevationmodel.sip
#    new file:   python/analysis/qgserror.sip
#    new file:   python/analysis/qgserrorlist.sip
#    new file:   python/analysis/qgsgcp.sip
#    new file:   python/analysis/qgsgcpset.sip
#    new file:   python/analysis/qgsgeoreferencer.sip
#    new file:   python/analysis/qgshasher.sip
#    new file:   python/analysis/qgsimageanalyzer.sip
#    new file:   python/analysis/qgsimagechip.sip
#    new file:   python/analysis/qgsimagefilter.sip
#    new file:   python/analysis/qgsmatrix.sip
#    new file:   python/analysis/qgsorthorectificationfilter.sip
#    new file:   python/analysis/qgsprojectionmanager.sip
#    new file:   python/analysis/qgsrasterdataset.sip
#    new file:   python/analysis/qgsrpcmodel.sip
#    new file:   python/analysis/qgssalientpoint.sip
#    new file:   python/analysis/qgssampler.sip
#    new file:   python/analysis/qgssensormodel.sip
#    new file:   python/analysis/qgssqldriver.sip
#    new file:   python/analysis/qgssqlitedriver.sip
#    new file:   python/analysis/qgswavelettransform.sip
#    new file:   python/plugins/autogcp/CMakeLists.txt
#    new file:   python/plugins/autogcp/__init__.py
#    new file:   python/plugins/autogcp/aboutdialog.py
#    new file:   python/plugins/autogcp/aboutdialogbase.ui
#    new file:   python/plugins/autogcp/autogcp.py
#    new file:   python/plugins/autogcp/databasedialog.py
#    new file:   python/plugins/autogcp/databasedialogbase.ui
#    new file:   python/plugins/autogcp/demdialog.py
#    new file:   python/plugins/autogcp/demdialogbase.ui
#    new file:   python/plugins/autogcp/drivers/CMakeLists.txt
#    new file:   python/plugins/autogcp/drivers/outputdrivers.db
#    new file:   python/plugins/autogcp/gcpitem.py
#    new file:   python/plugins/autogcp/gui.py
#    new file:   python/plugins/autogcp/guibase.ui
#    new file:   python/plugins/autogcp/help/.directory
#    new file:   python/plugins/autogcp/help/CMakeLists.txt
#    new file:   python/plugins/autogcp/help/DatabaseDialog
#    new file:   python/plugins/autogcp/help/ImageInfoDialog
#    new file:   python/plugins/autogcp/help/RectificationDialog
#    new file:   python/plugins/autogcp/help/SettingsDialog
#    new file:   python/plugins/autogcp/helpviewer.py
#    new file:   python/plugins/autogcp/helpviewerbase.ui
#    new file:   python/plugins/autogcp/icons/.directory
#    new file:   python/plugins/autogcp/icons/CMakeLists.txt
#    new file:   python/plugins/autogcp/icons/about.png
#    new file:   python/plugins/autogcp/icons/addgcp.png
#    new file:   python/plugins/autogcp/icons/algorithm.png
#    new file:   python/plugins/autogcp/icons/autogcp.png
#    new file:   python/plugins/autogcp/icons/connect.png
#    new file:   python/plugins/autogcp/icons/cross.png
#    new file:   python/plugins/autogcp/icons/database.png
#    new file:   python/plugins/autogcp/icons/delete.png
#    new file:   python/plugins/autogcp/icons/deleteall.png
#    new file:   python/plugins/autogcp/icons/disconnect.png
#    new file:   python/plugins/autogcp/icons/export.png
#    new file:   python/plugins/autogcp/icons/flagblue.png
#    new file:   python/plugins/autogcp/icons/flaggreen.png
#    new file:   python/plugins/autogcp/icons/flagred.png
#    new file:   python/plugins/autogcp/icons/flagyellow.png
#    new file:   python/plugins/autogcp/icons/foxhat.png
#    new file:   python/plugins/autogcp/icons/gcp.png
#    new file:   python/plugins/autogcp/icons/general.png
#    new file:   python/plugins/autogcp/icons/import.png
#    new file:   python/plugins/autogcp/icons/info.png
#    new file:   python/plugins/autogcp/icons/loaddb.png
#    new file:   python/plugins/autogcp/icons/metadata.png
#    new file:   python/plugins/autogcp/icons/movegcp.png
#    new file:   python/plugins/autogcp/icons/ortho.png
#    new file:   python/plugins/autogcp/icons/pan.png
#    new file:   python/plugins/autogcp/icons/pinblue.png
#    new file:   python/plugins/autogcp/icons/pingreen.png
#    new file:   python/plugins/autogcp/icons/pinred.png
#    new file:   python/plugins/autogcp/icons/pinyellow.png
#    new file:   python/plugins/autogcp/icons/projection.png
#    new file:   python/plugins/autogcp/icons/raster.png
#    new file:   python/plugins/autogcp/icons/removegcp.png
#    new file:   python/plugins/autogcp/icons/savedb.png
#    new file:   python/plugins/autogcp/icons/settings.png
#    new file:   python/plugins/autogcp/icons/symbology.png
#    new file:   python/plugins/autogcp/icons/unload.png
#    new file:   python/plugins/autogcp/icons/userinterface.png
#    new file:   python/plugins/autogcp/icons/zoomimage.png
#    new file:   python/plugins/autogcp/icons/zoomin.png
#    new file:   python/plugins/autogcp/icons/zoomout.png
#    new file:   python/plugins/autogcp/imagedialog.py
#    new file:   python/plugins/autogcp/imagedialogbase.ui
#    new file:   python/plugins/autogcp/marker.py
#    new file:   python/plugins/autogcp/progressdialog.py
#    new file:   python/plugins/autogcp/progressdialogbase.ui
#    new file:   python/plugins/autogcp/projectiondialog.py
#    new file:   python/plugins/autogcp/projectiondialogbase.ui
#    new file:   python/plugins/autogcp/rectificationdialog.py
#    new file:   python/plugins/autogcp/rectificationdialogbase.ui
#    new file:   python/plugins/autogcp/resources.qrc
#    new file:   python/plugins/autogcp/settings.py
#    new file:   python/plugins/autogcp/settingsdialog.py
#    new file:   python/plugins/autogcp/settingsdialogbase.ui
#    new file:   python/plugins/autogcp/xmlhandler.py
#    new file:   src/analysis/autogcp/qgsabstractoperation.h
#    new file:   src/analysis/autogcp/qgsautogcp.h
#    new file:   src/analysis/autogcp/qgsautogcpmanager.cpp
#    new file:   src/analysis/autogcp/qgsautogcpmanager.h
#    new file:   src/analysis/autogcp/qgsbilinearsampler.cpp
#    new file:   src/analysis/autogcp/qgsbilinearsampler.h
#    new file:   src/analysis/autogcp/qgscoordinatesystemtransform.cpp
#    new file:   src/analysis/autogcp/qgscoordinatesystemtransform.h
#    new file:   src/analysis/autogcp/qgscrosscorrelator.cpp
#    new file:   src/analysis/autogcp/qgscrosscorrelator.h
#    new file:   src/analysis/autogcp/qgsdatasource.cpp
#    new file:   src/analysis/autogcp/qgsdatasource.h
#    new file:   src/analysis/autogcp/qgselevationmodel.cpp
#    new file:   src/analysis/autogcp/qgselevationmodel.h
#    new file:   src/analysis/autogcp/qgserror.h
#    new file:   src/analysis/autogcp/qgserrorlist.cpp
#    new file:   src/analysis/autogcp/qgserrorlist.h
#    new file:   src/analysis/autogcp/qgsgcp.cpp
#    new file:   src/analysis/autogcp/qgsgcp.h
#    new file:   src/analysis/autogcp/qgsgcpset.cpp
#    new file:   src/analysis/autogcp/qgsgcpset.h
#    new file:   src/analysis/autogcp/qgsgcptransform.cpp
#    new file:   src/analysis/autogcp/qgsgcptransform.h
#    new file:   src/analysis/autogcp/qgsgeoreferencer.cpp
#    new file:   src/analysis/autogcp/qgsgeoreferencer.h
#    new file:   src/analysis/autogcp/qgshasher.cpp
#    new file:   src/analysis/autogcp/qgshasher.h
#    new file:   src/analysis/autogcp/qgsimageanalyzer.cpp
#    new file:   src/analysis/autogcp/qgsimageanalyzer.h
#    new file:   src/analysis/autogcp/qgsimagechip.cpp
#    new file:   src/analysis/autogcp/qgsimagechip.h
#    new file:   src/analysis/autogcp/qgsimagefilter.cpp
#    new file:   src/analysis/autogcp/qgsimagefilter.h
#    new file:   src/analysis/autogcp/qgsmatrix.cpp
#    new file:   src/analysis/autogcp/qgsmatrix.h
#    new file:   src/analysis/autogcp/qgsmatrix.h.astyle
#    new file:   src/analysis/autogcp/qgsorthorectificationfilter.cpp
#    new file:   src/analysis/autogcp/qgsorthorectificationfilter.h
#    new file:   src/analysis/autogcp/qgspointsampler.cpp
#    new file:   src/analysis/autogcp/qgspointsampler.h
#    new file:   src/analysis/autogcp/qgspostgresdriver.cpp
#    new file:   src/analysis/autogcp/qgspostgresdriver.h
#    new file:   src/analysis/autogcp/qgsprojectionmanager.cpp
#    new file:   src/analysis/autogcp/qgsprojectionmanager.h
#    new file:   src/analysis/autogcp/qgsrasterdataset.cpp
#    new file:   src/analysis/autogcp/qgsrasterdataset.h
#    new file:   src/analysis/autogcp/qgsrpcmodel.cpp
#    new file:   src/analysis/autogcp/qgsrpcmodel.h
#    new file:   src/analysis/autogcp/qgssalientpoint.h
#    new file:   src/analysis/autogcp/qgssampler.h
#    new file:   src/analysis/autogcp/qgssensormodel.h
#    new file:   src/analysis/autogcp/qgssqldriver.cpp
#    new file:   src/analysis/autogcp/qgssqldriver.h
#    new file:   src/analysis/autogcp/qgssqlitedriver.cpp
#    new file:   src/analysis/autogcp/qgssqlitedriver.h
#    new file:   src/analysis/autogcp/qgstpstransform.cpp
#    new file:   src/analysis/autogcp/qgstpstransform.h
#    new file:   src/analysis/autogcp/qgswavelettransform.cpp
#    new file:   src/analysis/autogcp/qgswavelettransform.h
#
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#    modified:   .gitignore
#    modified:   CMakeLists.txt
#    modified:   images/splash/splash.png
#    modified:   images/splash/splash.xcf.bz2
#    modified:   ms-windows/Installer-Files/UnWelcomeFinishPage.bmp
#    modified:   ms-windows/Installer-Files/WelcomeFinishPage.bmp
#    modified:   ms-windows/Installer-Files/sidelogomaster.xcf.bz2
#    modified:   ms-windows/QGIS-Installer.nsi
#    modified:   ms-windows/quickpackage.sh
#    modified:   python/CMakeLists.txt
#    modified:   python/plugins/CMakeLists.txt
#    modified:   src/analysis/CMakeLists.txt

Finally you can git commit to save your patch into your local repo and then push on up to QGIS GH when you are ready.