refactor(paths): Consolodates with hierarchical path util

[dk19y]

Replace hardcoded path strings with a structured path management system that organizes paths by scope (workspace, global, application) and provides type-safe path resolution.

Key changes:

• Add new paths.rs module with PathResolver and scoped path builders
• Replace hardcoded strings with constants in workspace/global/application modules
• Migrate existing path functions to use new system while maintaining compatibility
• Add system_paths module for common system directories
• Update MCP config loading to use new path resolution

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