Swap reference for inline links in BOM notes and other instructions fixes

Reference-style links in BOM notes don't get rendered correctly. Inline links should work, and I've tested that in a separate project.

I've also corrected a few typos, linked to the forum from the "customisation", "troubleshooting" and "finished" pages, and made the logo hyperlink back to openflexure.org.

Closes #267 (closed) Closes #299 (closed) Closes #276 (closed)