Fix runtime errors and improve robustness in host configs and scripts

- Fix KeyError in julia.nix when Project.toml lacks deps table
- Fix incorrect uv args in python.nix (remove --run + --add-flags combination)
- Remove redundant 'uv add ipython' from sync branch in python.nix
- Fix relative paths in project-scripts.nix (./scripts -> ../scripts)
- Fix initProject.sh to check file existence before git add
- Add RVER validation in updateDeps.sh with proper error handling
- Add tool availability checks in updateDeps.sh (uv, julia, devenv)
- Add flake.nix backup before modification in updateDeps.sh
- Ensure updateDeps.sh runs from repository root

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>

templates/rde/hosts/julia.nix

@@ -49,7 +49,9 @@ config: pkgs: {
   pluto = let
     runPluto = ''
       import Pkg; import TOML; Pkg.instantiate();
-      if !isfile("Project.toml") || !haskey(TOML.parsefile(Base.active_project())["deps"], "Pluto")
+      proj = isfile("Project.toml") ? TOML.parsefile(Base.active_project()) : Dict();
+      deps = get(proj, "deps", Dict());
+      if !haskey(deps, "Pluto")
         Pkg.add("Pluto");
       end
       import Pluto; Pluto.run();

templates/rde/hosts/python.nix

@@ -37,17 +37,12 @@ config: pkgs: {
         echo "🐍 Launching Marimo..."
         echo "--------------------------------------------------------------------------"
       fi
+      uv run marimo edit "$@"
     '';
   in {
     enable = config.enabledLanguages.python;
     path = {
-      value = "${pkgs.uv}/bin/uv";
-      args = [
-        "--run"
-        "${marimoInit}"
-        "--add-flags"
-        "run marimo edit \"$@\""
-      ];
+      value = "${pkgs.writeShellScriptBin "marimo-wrapper" marimoInit}/bin/marimo-wrapper";
     };
   };
 
@@ -78,23 +73,16 @@ config: pkgs: {
       else
         echo "--------------------------------------------------------------------------"
         echo "🔄 Syncing existing project..."
-        echo "📦 Ensuring IPython is installed..."
-        uv add ipython
         uv sync
         echo "🐍 Launching IPython..."
         echo "--------------------------------------------------------------------------"
       fi
+      uv run ipython "$@"
     '';
   in {
     enable = config.enabledLanguages.python;
     path = {
-      value = "${pkgs.uv}/bin/uv";
-      args = [
-        "--run"
-        "${ipythonInit}"
-        "--add-flags"
-        "run ipython \"$@\""
-      ];
+      value = "${pkgs.writeShellScriptBin "ipy-wrapper" ipythonInit}/bin/ipy-wrapper";
     };
   };