Does a `.hidden` configuration file for Finder exist?
Use the "hidden" file flag for this:

chflags hidden file1.txt directory "something else hidden"


See the chflags man page for more info. To see which files are hidden (and other file flags), use ls -lO:

$ ls -lO
total 0
drwxr-xr-x@ 2 gordon  staff  hidden 68 Feb 27 00:52 directory
-rw-r--r--@ 1 gordon  staff  hidden  0 Feb 27 00:52 file1.txt
-rw-r--r--  1 gordon  staff  uchg    0 Feb 27 00:54 lockedfile.txt
-rw-r--r--@ 1 gordon  staff  hidden  0 Feb 27 00:52 something else hidden
-rw-r--r--  1 gordon  staff  -       0 Feb 27 00:53 visiblefile.txt


BTW the "@" is there to indicate files that have extended attributes -- the unix-style "hidden" flag also shows up as an old-MacOS-style Finder flag, which is now represented as a bit in the "com.apple.FinderInfo" extended attribute. You can see extended attributes as well with ls -lO@, and their contents with xattr -l filename:

$ ls -lO@ file1.txt
-rw-r--r--@ 1 gordon  staff  hidden  0 Feb 27 00:52 file1.txt
        com.apple.FinderInfo    32
$ xattr -l file1.txt 
com.apple.FinderInfo:
00000000  00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00  |........@.......|
00000010  00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  |................|
00000020


The "32" means there are 32 bytes of data in the "com.apple.FinderInfo" attribute, and in the full dump the hexadecimal "40" corresponds to the "Invisible" flag in the old-style FinderInfo (/FileInfo) data structure.