ExtractVirtualFileSystemResources does not set correct permissions

[ih0r-d]

Description

Permissions are now stored as VFS metadata and applied on extraction.
This fixes non-executable binaries after extractResources.

Type of change

• New feature (non-breaking change which adds functionality)

Related to #43

What is changed

Updated VirtualFileSystemImpl to support explicit POSIX file permissions as filesystem metadata instead of relying on implicit or hardcoded executable heuristics.

The VFS now:

• parses file and directory permissions from fileslist,
• stores permissions on VFS entries,
• applies permissions when extracting files and directories,
• uses declared permissions consistently for access and execution checks.

This makes VFS behavior deterministic and aligned with real filesystem semantics.

How Has This Been Tested?

• Ran existing VirtualFileSystem unit tests locally after updating them to reflect permission-based behavior.
• Added coverage for permission propagation during extraction.
• Verified behavior using local embedding examples that trigger VFS extraction.

Test Configuration:

• JDK: project default
• OS: Linux / macOS
• Build tool: Maven
• GraalPy: local build (SNAPSHOT)

Checklist

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests validating the new behavior
• New and existing unit tests pass locally
• Any dependent changes have been merged and published in downstream modules