Do the exact same thing again. The new binary will be copied over the old one.

git clone creates a copy of git repository node's source code is in cd node/ changes directory to the one you just created with those files ./configure checks for dependencies and creates a makefile make executes that makefile, which results in compiling the source code into binary executable(s), libraries and any other outputs ls -l lists the files in the current directory node runs the node binary executable you just compiled from source, to ensure the compilation was successful sudo make install copies the files you just created from the current directory to their permanent homes, /usr/local/bin and such The last step overwrites whatever's already there with what you just built.

MongoDB http://docs.mongodb.org/manual/tutorial/install-mongodb-on-ubuntu

default host: localhost port:27017

Ubuntu File permissions https://help.ubuntu.com/community/FilePermissions

MongoDb http://docs.mongodb.org/manual/tutorial/install-mongodb-on-windows/