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index.php randomly appears in friendly URLs

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Problem/Motivation

Intermittently, index.php appears in our friendly URLs and it's always in the same spot, right after the first slash like it would be if you weren't using friendly URLs. Example: www.marshall.usc.edu/index.php/some/pattern/page.

This is reported to happen on both apache and nginx.

Steps to reproduce

One way to replicate was posted by marcaddeo in #2642126-13: [regression] Rewriting allows index.php/foo/bar URLs to function

  1. Using drush, clear the cache. drush @site.alias cr
  2. Immediately go to http://your.site.com/index.php
  3. Hover over any menu links, they will now have index.php prefixed on all of them, e.g. /index.php/user/1
  4. Go to http://your.site.com/
  5. All cached generated links will still be prefixed with /index.php/, e.g. /index.php/user/1

Proposed resolution

TBA

Remaining tasks

TBA

User interface changes

API changes

Data model changes

Release notes snippet

Original Issue Summary
Please note that this issue affects more than one version of Drupal, and my selection of the path.module was only a guess at what might be responsible. It might be noteworthy to mention that we are using the Pathauto module.

Intermittently, index.php appears in our friendly URLs and it's always in the same spot, right after the first slash like it would be if you weren't using friendly URLs. Example: www.marshall.usc.edu/index.php/some/pattern/page

After much research I found that our site is not the only site experiencing this issue but no one seems to know exactly what causes it. From the threads I've been reading, there is speculation that the bug may not be in core itself, that it may be introduced by one or more modules. But in our case we're either not using one of the speculated modules, or disabling it didn't solve the issue.

Hence the reason I am creating this Issue Report. I don't think anyone would ever want /index.php/ included in their friendly URLs, so why not just add some code to core to make sure it doesn't do that, ever!!

What are the steps required to reproduce the bug?
Unknown

What behavior were you expecting?
/index.php/ should never be included in a URL path when friendly URLs and Pathauto are being used.

What happened instead?
I think we covered that.

Please include as much information as you can:
OS: nginx
webserver name and version: Unknown (this happens on sites on Platform.sh and Acquia though, for what that is worth)
PHP version: 7.X
Drupal version: We are on the latest release of 8, but I read threads of it happening on 7 too.
Drupal path: site (web) root
Everything else you might feel is relevant:
I provided everything I can think of, but I'd be happen to answer any questions that might help.


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