Files with same name but different extensions leads to unexpected behaviour

[chrisjsewell]

Describe the bug

If there are multiple files with the same name but different file extensions;
sphinx will silently choose only one to parse:

To Reproduce
Steps to reproduce the behavior:

Given I have an extension installed to parse md

with:

index.rst
a.md
a.rst

index.rst:

.. toctree::
    a.md

This will actually include a.rst in the document, not a.md

Expected behavior
A clear and concise description of what you expected to happen.

Ideally you would have a config option to specify the order of preference for file extensions,
or if not set, a warning would be logged.

Your project
Link to your sphinx project, or attach zipped small project sample.

First noted in:
executablebooks/MyST-NB#82 (comment)

Screenshots
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Environment info

• OS: Mac
• Python version: 3.7.6
• Sphinx version: 2.4.4
• Sphinx extensions: myst-parser

Additional context
Add any other context about the problem here.

• [e.g. URL or Ticket]