fix: resolve 500 error caused by <think> tags and markdown code fences in content field from reasoning models like MiniMax/GLM

feat(graph): implement pagination for fetching nodes and edges; add utility functions for streamlined data retrieval

fix(file_parser): handle non-UTF-8 encoded text files with automatic encoding detection

Add UTF-8 encoding support for Windows console in run.py and logger.py to prevent character encoding issues

Enhance backend functionality with OASIS simulation features

Enhance backend startup logging and API endpoint display

Introduce Project ID for context management, finalizing the stateful API pipeline from file submission to graph construction.