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While highlight group in .vimrc highlights patterns just fine, highlight groups in .vim/after/ftplugin folder does not seem to do anything. Is it normal?

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It is normal, you are not using the correct directory. See :h mysyntaxfile-add:

If you are mostly satisfied with an existing syntax file, but would like to
add a few items or change the highlighting, follow these steps:

1. Create your user directory from 'runtimepath', see above.

2. Create a directory in there called "after/syntax".  For Unix: >
    mkdir ~/.config/nvim/after
    mkdir ~/.config/nvim/after/syntax

3. Write a Vim script that contains the commands you want to use.  For
   example, to change the colors for the C syntax: >
    highlight cComment ctermfg=Green guifg=Green

4. Write that file in the "after/syntax" directory.  Use the name of the
   syntax, with ".vim" added.  For our C syntax: >
    :w ~/.config/nvim/after/syntax/c.vim

That's it.  The next time you edit a C file the Comment color will be
different.  You don't even have to restart Vim.

See :h mysyntaxfile-replace if you want to completely replace an existing syntax file.

| improve this answer | |
  • Ah, I see. Thanks. Didn't understand where to look in the help file. Related question (don't want to ask a separate question for this): Is there a simple way to toggle a highlighing group? Couldn't find anything in the help file. – Mahbub Alam Jun 2 at 16:17
  • These highlights will go away if I happen to source .vimrc again on a file, right? That's also normal? – Mahbub Alam Jun 2 at 17:02

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