There are several ways to achieve what you describe using the shell, but it all comes down at what exaclty are you after and what level of access you have to the folders in question and shell access.
As I understand you want to change the behavior of the server respect to these new generated files. But it depends on the user running the script or aplication, their relation to the user of the shell or ftp... the fact is what we really know about your problem is not yet complete.
You could, for example, give the ownership of the folder to the app user, but it could make problems with the shell user or ftp user if they are not the same.
For this you can use:
chown -R user:group /[path-to]/myfolder
[path-to] is should be changed to the path of the folder and myfolder to the actual folder on the machine, user and group should be changed respectively to the user and group of the user that runs the app or script. If your folder was for example "app" and is on the /var/www/ path on the remote machine, and the app is run by www-data user, then it should be then
chown -R www-data:www-data /var/www/app
But as I say, little we know about the specifics. So it could be that the problem is generated by a strict policy by the server administrator where the umask something like:
umask 333 or even worst
where the resulting permissions are something like r--r--r-- or r--------
but to deal with these you can put a temporary umask in your app, or set it on the env for the user of the app... but I really think this is really unprobable.(tell me if you need something like this to expand on this option)
another way is not granting entirely the ownership to the app user, but to use a group the app user belongs to and enable the s flag to allow every file in the directory to be automatically created with special grant permissions on the group.
first change the group ownership of the folder, like:
chown -R sameuser:newgroup /[path-to]/myfolder
then change the sgid bit of the folder
chmod g+s /[path-to]/myfolder
more about sgid on http://www.linuxnix.com/sgid-set-sgid-linuxunix/
SGID (Set Group ID up on execution) is a special type of file permissions given to a file/folder. Normally in Linux/Unix when a program runs, it inherits access permissions from the logged in user. SGID is defined as giving temporary permissions to a user to run a program/file with the permissions of the file group permissions to become member of that group to execute the file. In simple words users will get file Group’s permissions when executing a Folder/file/program/command.
But anyway, if i'm missing your point, consider that sometimes it helps to know a little bit more about the problem in question. Consider expanding your question a little with some other relevant information (like what kind of app, what you mean about solving with linux, like what user runs your app or do you even have shell access?)
Hope it helps anyway.