A directive can live in four contexts: server config, virtual host, directory (<Directory>, <Files>, <Location>, <If>) and .htaccess. For each request Apache 129 merges the matching sections in a fixed order, and a later section overrides an earlier one. The order depends on the section type, not on where the section sits in the file; within each step, server-wide sections apply before the virtual host's.

To prove the order, each section below appends its name to a response header, written backward:
<VirtualHost *:8101>
ServerName site-a.example
DocumentRoot /var/www/site-a
<If "%{QUERY_STRING} =~ /debug/">
Header append X-Order "If"
</If>
<Location "/docs">
Header append X-Order "Location"
</Location>
<Files "*.html">
Header append X-Order "Files"
</Files>
<DirectoryMatch "^/var/www/site-a/docs">
Header append X-Order "DirectoryMatch"
</DirectoryMatch>
<Directory "/var/www/site-a">
AllowOverride FileInfo
Header append X-Order "Directory"
</Directory>
</VirtualHost>
<Directory "/var/www/site-a">
Header append X-Order "Directory (server)"
</Directory>A one-line docs/.htaccess adds Header append X-Order ".htaccess". With mod_headers enabled (Modules), three requests show which sections matched, in order:
curl -sI -H 'Host: site-a.example' 'localhost:8101/docs/page.html?debug=1' | grep X-Order
curl -sI -H 'Host: site-a.example' localhost:8101/docs/page.html | grep X-Order
curl -sI -H 'Host: site-a.example' localhost:8101/index.html | grep X-OrderX-Order: Directory (server), Directory, .htaccess, DirectoryMatch, Files, Location, If X-Order: Directory (server), Directory, .htaccess, DirectoryMatch, Files, Location X-Order: Directory (server), Directory, Files
The server-wide <Directory> ran first although it comes last in the file, and .htaccess overrode <Directory> but lost to every later step. Because <Location> and <If> merge last, a Require all granted in either silently cancels a <Directory> restriction, so keep access control in filesystem sections (Directory, Files, Location). Merging and Inheritance extends this to nested .htaccess files.