First thing is to download the zip file from GH again:

https://github.com/SimpleMachines/SMF2.1

Put it on your desktop and create a new folder beside it. It does not matter what you name it. Open the zip and extract to the new folder these folders:

Sources
Themes

(The reason we are not uploading all the folders like attachments is because if you do you will overwrite what you have, which would not be good.)

Now you need the files:

agreement.txt. (Only use this if you have not modified the copy you are already using.)
cron.php
index.php
proxy.php
SSI.php
ssi_examples.php
ssi_examples.shtml
subscriptions.php

Next, open the "other" folder in the zip file. You need to place certain files from here into the new folder with the index.php file. The files you need from here are:

db_last_error.php
upgrade.php
upgrade-helper.php

And just for good measure take all the files that end in .sql. Now, in your new folder you created on your desktop it should look like this:

Sources (folder)
Themes (folder)
agreement.txt.
cron.php
index.php
proxy.php
SSI.php
ssi_examples.php
ssi_examples.shtml
subscriptions.php

db_last_error.php
upgrade.php
upgrade-helper.php

upgrade_1-0.sql
upgrade_1-1.sql
upgrade_2-0_mysql.sql
upgrade_2-0_postgresql.sql
upgrade_2-1_mysql.sql
upgrade_2-1_postgresql.sql

If this is what you have than go ahead and zip it up. So now you have made your own zip file for updating your forum. All that is left to do now is get the forum ready.

How we do that is by backing up the database, uninstalling ALL mods, even if they error, saving any files you have done custom edits to and putting them all nicely on your desktop. So once you are sure you have everything backed up and stored in a safe place, go ahead and upload the zip file YOU created.

Once it's uploaded all that needs to be done is extract it and overwrite the folders and files that are on your server. Point your browser to www.yoursite.com/upgrade.php and your off.

I hope this helps out a bit keep all of you up to date from GH. Alternatively, you can download an nightly build from Simple machines and skip making your own zip folder. The choice is yours. By doing it this way I am guaranteed that all I am getting uploaded to my site is what I want to be overwritten, nothing else.