Migrate IndexedRepository model to Pydantic v2 configuration

[coderabbitai]

Description

The IndexedRepository model in backend/app/models/database/supabase.py currently uses Pydantic v1-style configuration (Config.orm_mode = True), which will be ignored under Pydantic v2.

Required Changes

Replace the v1-style config with v2-style configuration:

# Add import at top of file
from pydantic import ConfigDict

# In IndexedRepository class, replace:
class Config:
    orm_mode = True

# With:
model_config = ConfigDict(from_attributes=True)

Additional Scope

Review all other models in the same file and across the codebase for similar v1-style configurations that need migration.

Context

This issue was identified during the review of PR #138.

Related PR: #138
Review Comment: #138 (comment)
Requested by: @smokeyScraper

[smokeyScraper]

This issue, in fact, needs to address all warnings and dead code throughout the codebase while ensuring a robust system with minimal warnings—moreover, a cleanup issue.
Should include proper use of dotenv throughout too, as currently it's not very well organized (some files use os.getenv)

[PinJinx]

Hi @smokeyScraper , Could i work on this issue?

[smokeyScraper]

yepp @PinJinx, you can work on the issue.
Please ensure the above-mentioned request in the thread, there might be multiple warnings throughout the system even when using some specific handlers too. Please address them carefully.