Issue Title

parseAllowedTools() regex pattern order causes wrong flag to be matched with mixed quotes

Issue Body

Bug Description

parseAllowedTools() in src/modes/agent/parse-tools.ts checks regex patterns in a specific order:

1. Double-quoted: --allowed-tools "value"
2. Single-quoted: --allowed-tools 'value'
3. Unquoted: --allowed-tools value

This means if the input has mixed quote styles, it matches the first occurrence of the quote style checked first, not the first --allowed-tools flag in the string.

Reproduction

const input = `--allowed-tools 'mcp__github_inline_comment__create_inline_comment'
--allowed-tools 'mcp__context7__*'
--allowed-tools "Write,Edit,MultiEdit"`;

parseAllowedTools(input);
// Expected: ['mcp__github_inline_comment__create_inline_comment']
// Actual:   ['Write', 'Edit', 'MultiEdit']

Even though mcp__github_inline_comment__* is the FIRST flag in the string, the double-quoted pattern is checked first and matches "Write,Edit,MultiEdit".

Impact

This breaks the workaround for #800 (putting mcp__github_* tools first). Users must also ensure they use double quotes for the first flag, which is non-obvious.

The MCP server initialization depends on parseAllowedTools() finding mcp__github_* tools. When it finds the wrong value, the github_inline_comment server is not configured, and the tool becomes unavailable.

Workaround

Use double quotes for the mcp__github_* tools:

claude_args: |
  --allowed-tools "mcp__github_inline_comment__create_inline_comment"  # Double quotes!
  --allowed-tools 'mcp__context7__*'
  --allowed-tools "Write,Edit,MultiEdit"

Suggested Fix

Option 1: Find the actual first --allowed-tools in the string regardless of quote style:

const allPatterns = /--(?:allowedTools|allowed-tools)\s+(?:"([^"]+)"|'([^']+)'|([^\s]+))/g;
// Find the match with the smallest index

Option 2: The fix in PR #801 (parsing ALL flags) would also solve this, since all values would be accumulated.

Related Issues

• parseAllowedTools() only parses first --allowed-tools flag, breaking GitHub MCP server initialization #800 - Original report about only parsing first flag
• fix: parse ALL --allowed-tools flags, not just the first one #801 - PR to fix by parsing all flags
• shell-quote treats # as comment, swallowing all subsequent flags in claude_args #802 - shell-quote comment handling bug