This is a little off topic, but I have the same problem on Windows. I had a batch file named ctags.bat that contained the following line:
"C:\SOME_DIRECTORY\Vim Tools\ctags.exe" --options="%CD%\ctags.cnf"
This line has been expanded to:
"C:\SOME_DIRECTORY\Vim Tools\ctags.exe" --options="MY_CURRENT_DIRECTORY\ctags.cnf"
Ctags gave me the same error:
ctags.exe: cannot open option file "MY_CURRENT_DIRECTORY\ctags.cnf" : No such file or directory
Exiting the last \ made it work, i.e. I changed the line to:
"C:\SOME_DIRECTORY\Vim Tools\ctags.exe" --options="%CD%\\ctags.cnf"
Pay attention to \\ before ctags.cnf
Regarding your linux problem: try adding quotes around ".ctags":
ctags --options='./.ctags'
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