Do not forget, according to gitignore, that there is an order of precedence in the different "ignore pattern sources" that Git consider:
Patterns read from the command line for those commands that support them.
Patterns read from a .gitignore file in the same directory as the path, or in any parent directory, with patterns in the higher level files (up to the root) being overridden by those in lower level files down to the directory containing the file.
Patterns read from $GIT_DIR/info/exclude.
Patterns read from the file specified by the configuration variable core.excludesfile.
The last two can be a solution for your problem but:
they are not replicated for a distant repository
they can have their patterns overridden by the other sources
Ignore local changes to tracked files:
git update-index --assume-unchanged my-file.php
Unignore local changes to tracked files:
git update-index --no-assume-unchanged my-file.php
source: git help update-index
--[no-]assume-unchanged
...
This option can be also used as a coarse file-level mechanism to ignore uncommitted changes in tracked
files (akin to what .gitignore does for untracked files). Git will fail (gracefully) in case it needs to
modify this file in the index e.g. when merging in a commit; thus, in case the assumed-untracked file is
changed upstream, you will need to handle the situation manually.
If you just want to have some local files in the repository and the subdirectory location is flexible, you can put your files in tracked_dir1/tracked_dir2/untracked_dir/ and then add a tracked_dir1/tracked_dir2/untracked_dir/.gitignore with contents like:
I have been in similar situations, so I'm adding my preferred solution that I don't see mentioned. The problem with git update-index --assume-unchanged in this case is that you cannot do that for an untracked file. You said
I cannot modify the .gitignore of my repository.
I'm going to assume what you mean is that you can't push any changes to .gitignore to origin. If that is the case what you can do is add the untracked file to your local .gitignore, then do git update-index --assume-unchanged .gitignore so that your change to .gitignore is never pushed. Now you are ignoring the (possibly) untracked file, and not affecting the remote .gitignore file.