docs: small updates on documentation

[pamfilos]

• add section explaining JSON-Schemas ( validation, structure of metadata, links etc)
• explain analysis type ( ? - for now it’s only one per experiment)
• add info (per command) on access/permissions needed for each action
• analysis delete mention that published analysis cannot be deleted (since freezed)
• add info about ‘publishing’, ‘snapshots’, other concepts… ( we should say bit more about publishing, what it is, what consequences it has, snapshots, permissions, etc. It's a nice place to clarify some things that may be confusing for user) - maybe it should just be a link to this topic In general documentation (needed there also)
• analysis get change above -> below (since “options” went last) - same for published - check all over
• file commands
  • remove “—yes-i-know” from example ( all over documentation) - better get “prompted“
• Update some titles from “###” -> “####” (to be h3 instead of h4 - mainly for right sidebar navigation)
• Update repositories text eg.:
  • “the users can easily define certain git actions”)
  • “The user can specify in which event the repo will get updated on the CAP server.” -> not CAP server but in a CAP analysis..find better wording
• Update glossary terms

We should take in consideration what we document in the general documentation (or will document in the future), so we can point accordingly with some links. This way main "CAP concepts" won't be only on the CLI docs.

[Lilykos]

The previous/next buttons seem to need some work regarding where they point, most probably a fix with the headers markdown.

The repository & remove permissions titles should be reworded a bit, in order to become smaller and fit in the previous/next boxes.

[ArtemisLav]

In addition to all this, it would be useful if the CAP logo was clickable and took you back to the intro page.