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

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

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

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

Additional details and impacted files

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

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