Mend these broken links

[twalsh-ebi]

Description

This PR applies updates to Compara web docs, primarily to mend broken links and to replace HTTP URLs with their HTTPS equivalent (if available).

Other changes include:

• replacing reference links with anchor links consisting of a square bracket-enclosed reference number, consistent with the style used in hmm_lib.html;
• updating link context if necessary to reflect changes to the link or its destination;
• using relative links where possible;
• removing the reference to the codeml.ctl.hash file, which is no longer in the specified location; and
• correcting typos.

Views affected

These changes affect Compara web documentation, particularly the Comparative Genomics pages and Compara API Tutorial.

Possible complications

None expected.