Consolidate logging.basicConfig() calls to a single entry point

[gkorland]

Description

logging.basicConfig() is called in 8 separate modules under api/:

• api/index.py:22
• api/graph.py:9
• api/project.py:16
• api/analyzers/source_analyzer.py:21
• api/git_utils/git_graph.py:9
• api/git_utils/git_utils.py:15
• api/info.py:7
• api/llm.py:23

Only the first call to logging.basicConfig() takes effect (subsequent calls are silently ignored unless force=True is passed). This means the log configuration depends on whichever module is imported first, leading to unpredictable behavior.

Suggested Fix

1. Keep a single logging.basicConfig() call in api/index.py (the application entry point).
2. In other modules, use logger = logging.getLogger(__name__) without calling basicConfig().

Context

Found during code review of PR #522.