Issue 70: Restructure stan code

[seabbs]

Description

This PR closes #70 by restructuring the stan code. It does this by moving all stan functions in a stan/functions folder, updating the pathing of tools to respect this, and moving the cmdstan model into stan. Due to the pathing changes this has no impact on R facing usage.

Checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have included the target issue or issues in the PR title in the for Issue(s) issue-numbers: PR title
• I have read the contribution guidelines.
• I have tested my changes locally.
• I have added or updated unit tests where necessary.
• I have updated the documentation if required.
• My code follows the established coding standards.
• I have added a news item linked to this PR.
• I have reviewed CI checks for this PR and addressed them as far as I am able.

[seabbs]

LGTM (self-review)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.35%. Comparing base (14f259a) to head (89e7035).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #123   +/-   ##
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  Coverage   99.35%   99.35%           
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  Files          10       10           
  Lines         463      463           
=======================================
  Hits          460      460           
  Misses          3        3           

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