Update Ruff Rules

[caseyhans]

Update code base to accept previously ignored ruff rules.

• Return errors when caught and raised
• Unused iterable variable names prefixed with underscores
• Add a 15 second timeout to any GET and POST requests

Notes on other ignored rules:
S308: using mark_safe
- we use this a lot in template tags
- HERO uses a custom HTML sanitizer that calls mark_safe, which is then flagged as safe inline
- We could use this approach, or flag all our mark_safes inline

S314: raised when parsing XML input; I believe it'd require a new package to solve (defusedxml)
- 4 cases; could flag inline & remove from ignore list
- 3 cases are from parsing pubmed imports, one other is in a lit migration (0012) that parses HERO/RIS

S603: executing subprocess calls on "untrusted" inputs
- 4 cases; could be flagged as safe inline
- two of these cases are in the assessment_db_dump.py command for getting the db name from settings
- two of these are in the git.py commit model that returns last commit info; runs "git log" and grabs output

RUF012: 825 errors. too many to fix. related to mutable class attribute annotations

RUF015: iteration check; 3 failing cases, could be flagged safe inline

[munnsmunns]

Looks good to merge, nice job!