docs(configuration): rewrite configuration.md to reflect actual Python framework architecture

[tjsasakifln]

Summary

• Rewrites docs/configuration.md to document the actual Python-based framework instead of a non-existent Node.js/Docker/React/PostgreSQL stack
• Covers environment variables, agent config.py, agent.json schema, MCP server configuration, file-based storage, IDE setup, security best practices, and troubleshooting
• All content verified against actual codebase (.env.example, ENVIRONMENT_SETUP.md, os.environ usage in core/)

Fixes #1332

What changed

The previous configuration.md described infrastructure that does not exist in this project (Docker Compose, PostgreSQL, Redis, React frontend, JWT/CORS, honeycomb/ directory). This rewrite replaces every section with accurate documentation:

Section	Before (wrong)	After (correct)
Overview	Docker + Node.js + PostgreSQL	Environment vars + Agent config + pyproject.toml + .mcp.json
Environment	DATABASE_URL, JWT_SECRET, CORS_ORIGIN	ANTHROPIC_API_KEY, OPENAI_API_KEY, BRAVE_SEARCH_API_KEY, MOCK_MODE
Database	PostgreSQL schema, migrations, connection pooling	File-based persistence via framework.storage.FileStorage
Frontend	React, Vite, theme config	N/A (CLI-only project)
Agent config	N/A	config.py per agent, agent.json graph spec
MCP	N/A	.mcp.json server configuration
IDE	N/A	VS Code and PyCharm source root setup
Troubleshooting	N/A	ModuleNotFoundError, API key, agent resolution

No links to configuration.md from other files (README translations, DEVELOPER.md) were broken since the file path is preserved.

Test plan

• Verify every environment variable listed exists in .env.example or codebase os.environ calls
• Verify every file path referenced (exports/, config.py, agent.json, .mcp.json) exists in the repo
• Verify no references to removed concepts (Docker, PostgreSQL, React, honeycomb) remain
• Verify all cross-references from README translations and DEVELOPER.md still resolve

[bryanadenhq]

it looks great, thanks for your contribution!

[bryanadenhq]

Hi @tjsasakifln, there seems to be a merge conflict, could you please rebase with main before I merge? Thanks!

[tjsasakifln]

@bryanadenhq Thanks for the review and the heads-up on the merge conflict! Rebased on main — should be clean to merge now.

[IBOCATA]

Information-API & Infra-Energy Optimisation

Overview

This project integrates information theory, thermodynamics, statistics, quantum principles, and distributed systems security into one framework.

Components

• Shannon Entropy → Optimises information flow in APIs.
• Thermodynamic Entropy → Models infra-energy efficiency.
• P-value Analysis → Validates statistical significance of human judgement in LLM outputs.
• MCMC Simulation → Models uncertainty in decision-making.
• Kafka + Turing Machine Security → Ensures secure message passing with Schrödinger’s cat principle (secure/insecure until consumed).
• Terraform Automation → Deploys infrastructure automatically.

Usage

1. Run python main.py to execute entropy, statistical, and MCMC simulations.
2. Ensure Kafka is running locally for the security demo.
3. Deploy infra with:

   terraform init
   terraform apply