[Flow] composer update with self modified files (domainfactory hosting)

[Simon Schaufelberger (Schaufi)]

hello,
i'm running neos on a webserver of domainfactory where i needed to make 
a modifications on the "flow" file (have to change the path to php).

now when i do:
composer update

the file gets always overwritten even if there are no changes.

what exactly does composer here? i thought its just executing a git pull 
in all the repos. can somebody explain, how to use composer? please 
don't just point me to the composer website, i know where to find the 
manual but its really complicated to understand all the parameters and 
which one to use in which case.

my second question is how to add a new dependency.

as an example, i want to include:
git://git.typo3.org/FLOW3/Packages/TYPO3.SwiftMailer.git

what are the commands to do that?

sadly there is NO documentation on wiki.typo3.org at all...
-- 
Regards, Schaufi