id	summary	reporter	owner	description	type	status	priority	milestone	component	version	severity	resolution	keywords	cc
21372	flush_rewrite_rules() completely overwrites .htaccess	rulatir		"A call to flush_rewrite_rules(true) does a very unexpected and potentially destructive thing: it completely overwrites .htaccess.

While this probably isn't stated outright anywhere in the docs, the presence of the BEGIN/END delimiters yields a strong impression that it is safe to add directives to .htaccess outside the delimited Wordpress section.

If overwriting the whole .htaccess is by design and not a bug, then the format of generated .htaccess should be changed. Instead of the BEGIN/END comments misleading the developer into thinking that directives outside of that section will be preserved, it should contain an EXPLICIT STERN WARNING that the file is auto-generated and all changes made to it will be lost.
"	defect (bug)	closed	normal		Rewrite Rules		major	duplicate	reporter-feedback