RewriteRule ^ index.php [L] affecting 301 redirect - .htaccess

Question

I have a Drupal 7 website with several 301 redirects, however we've recently noticed an odd issue... When typing the url into your browser, it will not work if you include www.
www.example.com/something redirects to https://www.example.com/index.php
Using https://wheregoes.com/retracer.php the results for the above are:
http://www.example.com/something
301 Redirect -> http://www.example.com/here/something
301 Redirect -> https://www.example.com/index.php
example.com/someting will redirect correctly to https://www.example.com/here/something
Using https://wheregoes.com/retracer.php the results for the above are:
http://example.com/something
301 Redirect -> https://www.example.com/something
301 Redirect -> https://www.example.com/here/something
https://www.example.com/here/something is the expected endpoint.
From digging in my htaccess the issue appears to be with the standard Drupal 7 RewriteRule ^ index.php [L] line; however if I remove this I cannot log into the admin area.
Any thoughts on how this can be resolved? The SSL is only installed on www.example.com, so we need to redirect users to www.example.com and apply the SSL there. example.com has no SSL and unfortunately we cannot control this.
Below is my htaccess file:
#
# Apache/PHP/Drupal settings:
#
# Protect files and directories from prying eyes.
<FilesMatch "\.(engine|inc|info|install|make|module|profile|test|po|sh|.*sql|theme|tpl(\.php)?|xtmpl)(~|\.sw[op]|\.bak|\.orig|\.save)?$|^(\.(?!well-known).*|Entries.*|Repository|Root|Tag|Template|composer\.(json|lock))$|^#.*#$|\.php(~|\.sw[op]|\.bak|\.orig\.save)$">
<IfModule mod_authz_core.c>
Require all denied
</IfModule>
<IfModule !mod_authz_core.c>
Order allow,deny
</IfModule>
</FilesMatch>
# Don't show directory listings for URLs which map to a directory.
Options -Indexes
# Follow symbolic links in this directory.
Options +FollowSymLinks
# Make Drupal handle any 404 errors.
ErrorDocument 404 /index.php
# Set the default handler.
DirectoryIndex index.php index.html index.htm
# Override PHP settings that cannot be changed at runtime. See
# sites/default/default.settings.php and drupal_environment_initialize() in
# includes/bootstrap.inc for settings that can be changed at runtime.
# PHP 5, Apache 1 and 2.
<IfModule mod_php5.c>
php_flag magic_quotes_gpc off
php_flag magic_quotes_sybase off
php_flag register_globals off
php_flag session.auto_start off
php_value mbstring.http_input pass
php_value mbstring.http_output pass
php_flag mbstring.encoding_translation off
</IfModule>
# Requires mod_expires to be enabled.
<IfModule mod_expires.c>
# Enable expirations.
ExpiresActive On
# Cache all files for 2 weeks after access (A).
ExpiresDefault A1209600
<FilesMatch \.php$>
# Do not allow PHP scripts to be cached unless they explicitly send cache
# headers themselves. Otherwise all scripts would have to overwrite the
# headers set by mod_expires if they want another caching behavior. This may
# fail if an error occurs early in the bootstrap process, and it may cause
# problems if a non-Drupal PHP file is installed in a subdirectory.
ExpiresActive Off
</FilesMatch>
</IfModule>
# Various rewrite rules.
<IfModule mod_rewrite.c>
RewriteEngine on
# Set "protossl" to "s" if we were accessed via https://. This is used later
# if you enable "www." stripping or enforcement, in order to ensure that
# you don't bounce between http and https.
RewriteRule ^ - [E=protossl]
RewriteCond %{HTTPS} on
RewriteRule ^ - [E=protossl:s]
# Make sure Authorization HTTP header is available to PHP
# even when running as CGI or FastCGI.
RewriteRule ^ - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]
# Block access to "hidden" directories whose names begin with a period. This
# includes directories used by version control systems such as Subversion or
# Git to store control files. Files whose names begin with a period, as well
# as the control files used by CVS, are protected by the FilesMatch directive
# above.
#
# NOTE: This only works when mod_rewrite is loaded. Without mod_rewrite, it is
# not possible to block access to entire directories from .htaccess, because
# <DirectoryMatch> is not allowed here.
#
# If you do not have mod_rewrite installed, you should remove these
# directories from your webroot or otherwise protect them from being
# downloaded.
RewriteRule "/\.|^\.(?!well-known/)" - [F]
# If your site can be accessed both with and without the 'www.' prefix, you
# can use one of the following settings to redirect users to your preferred
# URL, either WITH or WITHOUT the 'www.' prefix. Choose ONLY one option:
#
# To redirect all users to access the site WITH the 'www.' prefix,
# (http://example.com/... will be redirected to http://www.example.com/...)
# uncomment the following:
# RewriteCond %{HTTP_HOST} .
# RewriteCond %{HTTP_HOST} !^www\. [NC]
# RewriteRule ^ http%{ENV:protossl}://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]
#
# To redirect all users to access the site WITHOUT the 'www.' prefix,
# (http://www.example.com/... will be redirected to http://example.com/...)
# uncomment the following:
# RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]
# RewriteRule ^ http%{ENV:protossl}://%1%{REQUEST_URI} [L,R=301]
# Modify the RewriteBase if you are using Drupal in a subdirectory or in a
# VirtualDocumentRoot and the rewrite rules are not working properly.
# For example if your site is at http://example.com/drupal uncomment and
# modify the following line:
# RewriteBase /drupal
#
# If your site is running in a VirtualDocumentRoot at http://example.com/,
# uncomment the following line:
# RewriteBase /
# Pass all requests not referring directly to files in the filesystem to
# index.php. Clean URLs are handled in drupal_environment_initialize().
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^ index.php [L]
# Rules to correctly serve gzip compressed CSS and JS files.
# Requires both mod_rewrite and mod_headers to be enabled.
<IfModule mod_headers.c>
# Serve gzip compressed CSS files if they exist and the client accepts gzip.
RewriteCond %{HTTP:Accept-encoding} gzip
RewriteCond %{REQUEST_FILENAME}\.gz -s
RewriteRule ^(.*)\.css $1\.css\.gz [QSA]
# Serve gzip compressed JS files if they exist and the client accepts gzip.
RewriteCond %{HTTP:Accept-encoding} gzip
RewriteCond %{REQUEST_FILENAME}\.gz -s
RewriteRule ^(.*)\.js $1\.js\.gz [QSA]
# Serve correct content types, and prevent mod_deflate double gzip.
RewriteRule \.css\.gz$ - [T=text/css,E=no-gzip:1]
RewriteRule \.js\.gz$ - [T=text/javascript,E=no-gzip:1]
<FilesMatch "(\.js\.gz|\.css\.gz)$">
# Serve correct encoding type.
Header set Content-Encoding gzip
# Force proxies to cache gzipped & non-gzipped css/js files separately.
Header append Vary Accept-Encoding
</FilesMatch>
</IfModule>
</IfModule>
# Add headers to all responses.
<IfModule mod_headers.c>
# Disable content sniffing, since it's an attack vector.
Header always set X-Content-Type-Options nosniff
</IfModule>
<IfModule mod_rewrite.c>
RewriteEngine on
Redirect 301 /examplelink.php /example-link
Redirect 301 /someoldlink.php /new/location
Redirect 301 /something /here/something
</IfModule>
RewriteEngine On
RewriteCond %{HTTPS} !on
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/\.well-known/pki-validation/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$
RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI} [L,R=301]

Answer 1

The problem you are probably having is that your 301 redirects are happening after your internal routing to the index.php page. Additionally, you're using the Redirect directive, which is mod_alias and not part of mod_rewrite. This means the same request gets processed twice, once by mod_alias and once by mod_rewrite. This is making it so an internal rewrite (to index.php) ends up getting redirected because mod_alias marked the request for a 301.
Remove these lines from the bottom of your .htaccess file:
<IfModule mod_rewrite.c>
RewriteEngine on
Redirect 301 /examplelink.php /example-link
Redirect 301 /someoldlink.php /new/location
Redirect 301 /something /here/something
</IfModule>
RewriteEngine On
RewriteCond %{HTTPS} !on
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/\.well-known/pki-validation/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$
RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI} [L,R=301]
Then under the first mod_rewrite block, which looks like this:
# Various rewrite rules.
<IfModule mod_rewrite.c>
RewriteEngine on
Add these lines under RewriteEngine on:
RewriteRule ^examplelink\.php$ /example-link [L,R=301]
RewriteRule ^someoldlink\.php$ /new/location [L,R=301]
RewriteRule ^something$ /here/something [L,R=301]
RewriteCond %{HTTPS} !on
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/\.well-known/pki-validation/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$
RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI} [L,R=301]