Fix links in README when rendered to github pages and other fixes/cleanup

[Ortonix]

Description:

Resolve Issue #109

I have deployed the edited code here so changes can be previewed live (original for comparison).

• Convert html links to markdown so they render back into html properly when being deployed to github-pages
  • This is needed so that a link to FAQ.md is detected and changed to link to the generated FAQ.html
• Fix list indenting to fit github markdown formatting rules
  • This one was a bit more odd - it seems that github pages uses a different markdown interpreter that takes a 4 space indent (beyond the level of the list) as a code block, which is why random parts of the BOM are currently showing as code blocks. This is now fixed.
  • I have kept indenting to 2 space tab stops to make editing easier.
• Add meaningful alt text to image links (where link was markdown)
• Change as much html to markdown as possible
  • Some html is used to centre items on the page and to constrain width of images this is not something markdown can do.
  • Image sizes should be set by uploading an image of the correct dimensions. This is out of scope of this PR.
• Tidy up markdown formatting
  • Blank lines around headers and lists
  • Remove trailing whitespace (except where needed)
  • Use _ for italics
• Add heading to FAQ

There may be a couple of conflicts between this and my other PR, but they will be easily resolved.

[AJ-Koenig]

LGTM - waiting for conflicts to be resolved.

[Ortonix]

Conflicts resolved and checked for issues on deployment here

Fixed one broken link.