fix: exclude node_modules from dependency analysis and add progress logging

[zhalice2011]

Problem

When running codewiki generate on a JavaScript/TypeScript project, the dependency analyzer processes all files in node_modules, resulting in 225,098 files being analyzed instead of the expected ~630 project source files.

The CLI correctly detects 623 TypeScript + 8 JavaScript files:

[22:06:19] Detected languages: TypeScript (623 files), JavaScript (8 files)

But the backend analyzer receives 225,098 files because node_modules is not excluded:

[22:07:35] 📊 Parsing 225098 source files (this may take a few minutes)...
[22:07:35]   [1/225098] .eslintrc.js

This causes the analysis to hang indefinitely with no progress feedback.

Root Cause

node_modules is missing from DEFAULT_IGNORE_PATTERNS in patterns.py. The CLI file detection (validation.py) has its own hardcoded exclusion set that correctly filters node_modules, but the backend dependency analyzer (repo_analyzer.py) relies on DEFAULT_IGNORE_PATTERNS which lacks it.

Solution

1. Add missing ignore patterns (patterns.py)

Added to DEFAULT_IGNORE_PATTERNS:

• node_modules / node_modules/ — the primary fix
• .next/ — Next.js build output
• .nuxt/ — Nuxt.js build output
• .turbo/ — Turborepo cache

2. Add progress logging and timeout protection (call_graph_analyzer.py)

• Per-file progress logging: Reports progress every 10% with elapsed time and ETA
• 30-second timeout per file: Prevents hanging on problematic files
• Failure statistics: Shows how many files succeeded/failed
• Total elapsed time: Reports overall analysis duration

Before:

[00:00]   Parsing source files...
(silence for 15+ minutes)

After:

📊 Parsing 631 source files (this may take a few minutes)...
  [1/631] src/index.ts (0.1s elapsed, ~120.0s remaining)
  [63/631] src/components/App.tsx (12.5s elapsed, ~108.0s remaining)
  ...
✓ Analysis complete: 630/631 files analyzed, 1 failed, 1234 functions, 567 relationships (95.3s)

Test plan

• codewiki generate --verbose on a TypeScript project with node_modules now analyzes only source files (~631 instead of 225,098)
• Progress logging shows per-file updates with elapsed time and ETA
• Files exceeding 30s timeout are skipped gracefully
• Non-verbose mode remains quiet (only warnings shown)