Add Copilot instructions, update flake.lock, and enhance Nix configurations

- Introduced Copilot instructions for better project understanding.
- Updated flake.lock with new dependency revisions and hashes.
- Modified zen.nix to include tracking protection and native messaging hosts.
- Added godot.nix for Godot language support in VSCode.
- Enhanced kde.nix with additional system packages and session variables.
- Created thunderbolt.nix to enable Thunderbolt services.
- Updated Bellerophon default.nix to include thunderbolt.nix.
- Adjusted hardware-configuration.nix to include new kernel modules and parameters.

.github/copilot-instructions.md

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+# Copilot Instructions for EmergentMind's Nix-Config
+
+## Project Overview
+- This is a modular, flake-based NixOS configuration system, designed for multi-host, multi-user, and reproducible setups.
+- Major directories:
+  - `hosts/`: Per-host NixOS configs (e.g., `hosts/nixos/Bellerophon/`).
+  - `home/`: Per-user Home Manager configs.
+  - `modules/`: Reusable NixOS and Home Manager modules, auto-imported via `lib.custom.scanPaths`.
+  - `overlays/`, `pkgs/`: Custom packages and overlays.
+  - `nixos-installer/`: Standalone flake for bootstrapping new hosts, with its own README and workflows.
+  - `docs/`: Project documentation, including secrets management.
+  - `scripts/`: Helper scripts for bootstrap, rebuild, sops, etc.
+
+## Key Patterns & Conventions
+- **Imports**: Use `lib.custom.relativeToRoot` and `lib.custom.scanPaths` for DRY, recursive module imports.
+- **Host/Module Structure**: Each host and user has a directory with a `default.nix` as entrypoint. Common/optional configs are split for clarity.
+- **Disk Layout**: Disk setup is handled by `disko` modules, with per-host overrides for device and swap.
+- **Secrets**: Secrets are managed via a private `nix-secrets` repo and sops-nix. See `docs/secretsmgmt.md` and `nixos-installer/README.md` for details.
+- **VSCode/Language Support**: Language-specific VSCode configs live in `home/panotaka/common/optional/coding/vscode/languages/` and are imported via the main VSCode module.
+
+## Developer Workflows
+- **Build & Rebuild**: Use `just rebuild` (runs pre/post hooks, see `justfile`). For full checks: `just rebuild-full` or `just check`.
+- **ISO Generation**: `just iso` builds a custom NixOS installer ISO.
+- **Secrets**: Use `just rekey`, `just sops-add-creation-rules`, and related commands for sops/age key management.
+- **Sync/Deploy**: Use `just sync` and `just build-host` for remote deployment.
+- **Testing**: Tests live in `tests/` and use `bats`.
+
+## Integration Points
+- **External**: Relies on `nix-secrets` (private), sops-nix, disko, stylix, nix4vscode, and nixos-hardware modules.
+- **Cross-Component**: Host configs import common modules and optional features via mapped imports. Home Manager and NixOS modules are kept separate but coordinated.
+
+## Examples
+- To add a new host: copy an existing host dir in `hosts/nixos/`, update disk and user settings, and add secrets as per `nixos-installer/README.md`.
+- To add a new language to VSCode: add a `.nix` file to `vscode/languages/` and import it in the main VSCode module.
+- To update secrets: run `just rekey` and follow the documented workflow.
+
+## References
+- See `README.md`, `nixos-installer/README.md`, and `docs/secretsmgmt.md` for deep dives on architecture and workflows.
+- For module patterns, see `modules/` and `hosts/common/core/`.
+
+---
+
+If you are unsure about a workflow or pattern, check the referenced docs or ask for clarification in your PR.