Many hosting configurations have something like a httpdocs directory for each site at the same level as logs, statistics, error_docs and other hosting related files.
So then you would set your FTP to reference the sites httpdocs directory and skip all of those other directories.
hosting_root
site1
error_docs
logs
httpdocs
site2
error_docs
logs
httpdocs |
If you are pointing your FTP at either hosting_root or site1/site2 then you would include files you probably do not want.
If your files are extensionless and you have tons of them then maybe they should really have extensions or some common naming so they can be identified/hidden using wildcards, or instead place them into directories that can be hidden. The only other alternative is to hide every file by its full name, but that sounds very tedious and maybe not possible.
For example, Magento keeps most of its variable data in a directory called
var and log files in
var/log so I can hide either of those in the project properties (Project > Content > Hide files / Hide directories) to stop those files being synced. PhpED does not need those files for any code insights, so hiding the var directory does not give any problems.