fix: parse ALL --allowed-tools flags, not just the first one

[AlexanderBartash]

Summary

Fixes #800

The parseAllowedTools() function previously used .match() which only returns the first match. This caused tools specified in subsequent --allowed-tools flags to be ignored during MCP server initialization.

Changes

• Add /g flag to regex patterns for global matching
• Use matchAll() to find all occurrences
• Deduplicate tools while preserving order
• Make unquoted pattern not match quoted values (to avoid capturing quotes from quoted patterns)

Root Cause

When users specify multiple --allowed-tools flags:

claude_args: |
  --allowed-tools 'mcp__context7__*'
  --allowed-tools 'Read,Glob,Grep'
  --allowed-tools 'mcp__github_inline_comment__create_inline_comment'

Only tools from the first flag were parsed. This broke MCP server initialization when mcp__github_* tools weren't in the first flag.

Test plan

• All existing tests pass
• Added new tests for multiple --allowed-tools flags
• Added test for deduplication across flags
• Added test for multiline flag parsing