Use dynamic RewriteBase that matches WP installation sub-directory.

See wpsharks/comet-cache#792

src/includes/templates/htaccess/canonical-urls-no-ts-enable.txt

@@ -1,7 +1,7 @@
 # Force NO trailing slash on all virtual requests (except WP admin area).
 <IfModule rewrite_module>
   RewriteEngine On
-  RewriteBase /
+  RewriteBase %%REWRITE_BASE%%
 
   # If not a real file or directory.
   RewriteCond %{REQUEST_FILENAME} !-f

src/includes/templates/htaccess/canonical-urls-ts-enable.txt

@@ -1,7 +1,7 @@
 # Force a trailing slash on all virtual requests (except WP admin area).
 <IfModule rewrite_module>
   RewriteEngine On
-  RewriteBase /
+  RewriteBase %%REWRITE_BASE%%
 
   # If not a real file or directory.
   RewriteCond %{REQUEST_FILENAME} !-f

src/includes/traits/Plugin/HtaccessUtils.php

@@ -107,6 +107,7 @@ public function addWpHtaccess()
             return true; // Nothing to do, but no failures either.
         }
 
+        $template_blocks           = $this->fillReplacementCodes($template_blocks);
         $template_header           = '# BEGIN '.NAME.' '.$this->htaccess_marker.' (the '.$this->htaccess_marker.' marker is required for '.NAME.'; do not remove)';
         $template_footer           = '# END '.NAME.' '.$this->htaccess_marker;
         $htaccess['file_contents'] = $template_header."\n\n".trim($template_blocks)."\n\n".$template_footer."\n\n".$htaccess['file_contents'];
@@ -223,6 +224,31 @@ public function findHtaccessMarker($htaccess_marker = '')
         return true; // Htaccess has the marker
     }
 
+    /**
+     * Utility method used to update replacement codes in .htaccess templates
+     *
+     * @since 16xxxx Adding Apache Optimizations
+     *
+     * @param string $template_blocks .htaccess template blocks that may contain replacement codes
+     *
+     * @return string Template blocks with replacement codes filled in
+     */
+    public function fillReplacementCodes($template_blocks)
+    {
+        if (mb_stripos($template_blocks, '%%') === false) {
+            return $template_blocks; // No replacement codes to fill
+        }
+
+        $replacement_codes = ['%%REWRITE_BASE%%' => trailingslashit(parse_url(home_url(), PHP_URL_PATH))];
+
+        foreach ($replacement_codes as $_code => $_replacement) {
+            $template_blocks = preg_replace('/'.preg_quote($_code, '/').'/ui', $_replacement, $template_blocks);
+        }
+        unset($_code, $_replacement);
+
+        return $template_blocks;
+    }
+
     /**
      * Gets contents of `/.htaccess` file with exclusive lock to read+write. If file doesn't exist, we attempt to create it.
      *

src/includes/traits/Plugin/WcpSettingUtils.php

@@ -25,6 +25,7 @@ public function autoClearCacheOnSettingChanges()
         $done = true; // Flag as having been done.
 
         if ($pagenow === 'options-general.php' && $settings_updated) {
+            $this->addWpHtaccess(); // Update .htaccess if applicable
             $counter += $this->autoClearCache();
         } elseif ($pagenow === 'options-reading.php' && $settings_updated) {
             $counter += $this->autoClearCache();