can I add that iml file to the file nesting? and how to do it?

yes, you can.
just add the file name x.iml to pubspec.yaml list in the snippet

as of v1.67.0, we can remove the experimental tag.

"explorer.fileNesting.enabled": true,
"explorer.fileNesting.expand": false,
"explorer.fileNesting.patterns": {
    "pubspec.yaml": ".flutter-plugins, .packages, .dart_tool, .flutter-plugins-dependencies, .metadata, .packages, pubspec.lock, build.yaml, analysis_options.yaml, all_lint_rules.yaml",
    ".gitignore": ".gitattributes, .gitmodules, .gitmessage, .mailmap, .git-blame*",
    "readme.*": "authors, backers.md, changelog*, citation*, code_of_conduct.md, codeowners, contributing.md, contributors, copying, credits, governance.md, history.md, license*, maintainers, readme*, security.md, sponsors.md",
    "*.dart": "$(capture).g.dart, $(capture).freezed.dart",
},

yup this worked!

To everyone, remove the word experimental — it doesn’t work anymore.
Use this instead 👇
"explorer.fileNesting.enabled": true,
"explorer.fileNesting.expand": false,
"explorer.fileNesting.patterns": {
"pubspec.yaml": ".flutter-plugins, .packages, .dart_tool, .flutter-plugins-dependencies, .metadata, .packages, pubspec.lock, build.yaml, analysis_options.yaml, all_lint_rules.yaml",
".gitignore": ".gitattributes, .gitmodules, .gitmessage, .mailmap, .git-blame*",
"readme.": "authors, backers.md, changelog, citation*, code_of_conduct.md, codeowners, contributing.md, contributors, copying, credits, governance.md, history.md, license*, maintainers, readme*, security.md, sponsors.md",
"*.dart": "$(capture).g.dart, $(capture).freezed.dart"
},