Fix and update URLs

[twalsh-ebi]

Description

This PR would fix and update various URLs in code and documentation.

This is not a comprehensive update: changes have been restricted to URLs likely to be accessed during production or by users.

Overview of changes

Changes include:

• addressing broken links by replacement with a suitable alternative or, in a minority of cases, removal;
• converting HTTP to HTTPS links where appropriate; and
• updating code that accesses a service for which the interface has changed (e.g. GetSpeciesList.pm, flatten_mouse_files.pl).

Testing

All updated URLs were checked for validity.

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For code reviewers: code review SOP

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 60.63%. Comparing base (869a769) to head (0256ab5).

Additional details and impacted files

@@               Coverage Diff               @@
##           release/115     #903      +/-   ##
===============================================
- Coverage        60.64%   60.63%   -0.01%     
===============================================
  Files              212      212              
  Lines            23028    23028              
  Branches          3632     3632              
===============================================
- Hits             13966    13964       -2     
  Misses            7843     7843              
- Partials          1219     1221       +2     

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