How do I make WordPress revise an .htaccess file a certain way?

Question

I've learned just a slight bit with WordPress Rewrite API -- just enough to add another rewrite rule for a plugin. The plugin works if installed in the root, but I'm finding that if one installs WordPress in a subdir, then I need to do the following changes to the .htaccess file. I'd like to know how to automate these changes if possible. As well, there's a second problem. If one goes to the Permalinks Settings in WordPress, my custom changes get overwritten (except for my special rule that uses WP Rewrite API). So, I need something that uses WordPress Rewrite API so that they don't get overwritten.

Original .htaccess file

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /mysubdir/
RewriteRule ^index\.php$ - [L]
# my special WP Rewrite API line
RewriteRule ^special(.*)$ /mysubdir/wp-content/plugins/special/app/$1 [QSA,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /mysubdir/index.php [L]
</IfModule>
# END WordPress

Changes I Made To Make Plugin Work in a Subdir

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On

#RewriteBase /mysubdir/

RewriteRule ^index\.php$ - [L]
# my special WP Rewrite API line
RewriteRule ^special(.*)$ /mysubdir/wp-content/plugins/special/app/$1 [QSA,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

#RewriteRule . /mysubdir/index.php [L]

RewriteRule . index.php [L]
</IfModule>
# END WordPress

Answer 1

If you don't want Wordpress to overwrite your changes in .htaccess file, then make sure that you write your changes outside of the Wordpress comment block, that is, either before or after this:

# BEGIN WordPress
...
# END WordPress

Think of this area as Wordpress' territory. Anything within this block, will be overwritten by Wordpress once it has to make any changes to .htaccess.

This is what you can do after the Wordpress comment block:

# BEGIN WordPress
...
# END WordPress

<IfModule mod_rewrite.c>
# Write your rewrite rules here.
</IfModule>

Answer 2

You can use add_rewrite_rule() to add rules to the .htaccess file. If you add these rules on init (or just prior to when the rules are flushed), then anytime the rules are flushed (i.e. when permalink settings are saved), those rules will be kept.

Note, typically a rewrite passed to add_query_arg is of the form:

'index.php?p=12&food=$matches[1]&variety=$matches[2]'

and WordPress handles it internally and does not add them to the .htaccess file. But if the first part is not index.php? then it is treated as an external rewrite rule and added to .htaccess. See source.