Update report template and vignette, add tests, update register output, support multiple repo types

[nuest]

Relevant changes:

• use a loop to create R Markdown output based on the files in the manifest list
• change the process to get the certificate number

[sje30]

will look at these changes next week (early) I hope.

[nuest]

now also support for multiple repo types

[nuest]

I hope this fixes the broken CI rendering of the register, see https://github.com/codecheckers/register/actions/runs/405869903