Using system version in .tool-versions still sets environment variables such as GOROOT and JAVA_HOME

[Frederick888]

Describe the bug
The environment variables point to literal system tool versions, which don't exist.

To Reproduce

$ cat .tool-versions
golang system
java system
$ command -v java
/usr/bin/java
$ echo $JAVA_HOME
/Users/frederick/.local/share/mise/installs/java/system
$ java -version
The operation couldn’t be completed. Unable to locate a Java Runtime.
Please visit http://www.java.com for information on installing Java.

$ command -v go
/usr/local/bin/go
$ echo $GOROOT
/Users/frederick/.local/share/mise/installs/go/system/go
$ go version
go: cannot find GOROOT directory: /Users/frederick/.local/share/mise/installs/go/system/go

Expected behavior
When using system version in .tool-versions, mise does not set the tool-specific environment variables.

mise doctor output

mise version:
  2024.1.30 macos-x64 (2024-01-27)

build:
  Target: x86_64-apple-darwin
  Features: DEFAULT, NATIVE_TLS
  Built: Sat, 27 Jan 2024 01:50:36 +0000
  Rust Version: rustc 1.75.0 (82e1608df 2023-12-21) (Homebrew)
  Profile: release

shell:
  /usr/local/bin/zsh
  zsh 5.9 (x86_64-apple-darwin21.3.0)

mise data directory:
  /Users/frederick/.local/share/mise

mise environment variables:
  MISE_SHELL=zsh

settings:
  {
    "activate_aggressive": false,
    "all_compile": false,
    "always_keep_download": false,
    "always_keep_install": false,
    "asdf_compat": false,
    "cargo_binstall": true,
    "color": true,
    "disable_default_shorthands": false,
    "disable_tools": [],
    "experimental": false,
    "jobs": 4,
    "legacy_version_file": true,
    "legacy_version_file_disable_tools": [],
    "node_compile": false,
    "not_found_auto_install": true,
    "paranoid": false,
    "plugin_autoupdate_last_check_duration": "7d",
    "python_compile": false,
    "python_default_packages_file": "/Users/frederick/.default-python-packages",
    "python_patch_url": null,
    "python_precompiled_os": null,
    "python_patches_directory": null,
    "python_precompiled_arch": null,
    "python_pyenv_repo": "https://github.com/pyenv/pyenv.git",
    "python_venv_auto_create": false,
    "raw": false,
    "shorthands_file": null,
    "status": {
      "missing_tools": true,
      "show_env": false,
      "show_tools": false
    },
    "task_output": null,
    "trusted_config_paths": [],
    "quiet": false,
    "verbose": false,
    "yes": false,
    "ci": false,
    "cd": null,
    "debug": false,
    "env_file": null,
    "trace": false,
    "log_level": "info"
  }

config files:

plugins:
  bun      (core)
  deno     (core)
  dhall    https://github.com/aaaaninja/asdf-dhall.git#bcf4b23
  go       (core)
  java     (core)
  node     (core)
  python   (core)
  ruby     (core)

toolset:


1 problem found:
shims are missing, run mise reshim to create them
Missing shims: wheneverize, knife, ddtracerb, multiruby, newrelic, foreman, pydoc3.8, gurl, godef, dlv, samlr, gdb_wrapper, elastic_ruby_console, rake-compiler, fission, danger, bump, mkdocs, stripe-mock-server, dhall-to-bash, yard, cucumber-html-formatter, chef-solo, python2.7, reek, maruku, rwinrm, packwerk, jenkinscli, rescue, sidekiqmon, asmfmt, npx, validate_string_sweep_files, deploy_catapult, dhall-to-nix, pip3.11, coveralls, rougify, restclient, ruby-rewrite, aws_sqs_active_job, idle, go, lessc, sdoc-merge, setup, github-markup, pydoc3, node, rbvmomish, motion, stripe-console, bundler-audit, rails-erb-lint, neovim-ruby-host, rb-sys-dock, user_agent_parser, unparser, bundle-audit, ruby_parse_extract_error, wwtd, pydoc3.11, htmldiff, safe_yaml, protoc-gen-beefcake, blade, watchmedo, gherkin-ruby, extlz4, ruby-prof-check-trace, slimrb, python3.11-config, redcarpet, cab, fillstruct, rollbar-rails-runner, zentest, y2racc, shopify, master_cut, bulk_test_account_uploader.rb, chef-apply, mongo_console, autospec, vim-flavor, newrelic_cmd, print_header.sh, mongrel_rpm, python2-config, marutex, idle3.9, geoip, dartsass, ldiff, python2.7-config, racecar, srb, pirb, rotp, mdl, yarv, python3, faker, spec, errcheck, openapi-to-dhall, python2, generate-api, haml, backburner, solargraph-runtime, term_colortab, fog, geocode, standardrb, mustache, stackprof-flamegraph.pl, gopls, slack, travis, puma, pre-commit, kramdown, 2to3-3.10, pip-sync, whenever, flay, csv-to-dhall, js-beautify, python3.10, pruby, scss, solargraph, pip3.9, easy_install-2.7, dhall-to-yaml-ng, unicorn, kill-pry-rescue, ruby-prof, patience_diff, iferr, qunit-selenium, dhall, ohai, dupfind, resque-web, jasmine, deadcode, pydoc, pip-compile, testrbl, python3.9-gdb.py, pumactl, haml-lint, pip3.8, m, thin, pronto, parallel_rspec, term_snow, testrb, commonmarker, tapioca, python3.10-gdb.py, gherkin, yardoc, rwinrmcp, rdiscount, python-config, gomodifytags, dkimsign.rb, 2to3-3.8, mixlib-install, xsd2ruby.rb, sidekiq, dhall-to-csv, voyager_cli, jekyll, python3.8, fauxhai, python3.8-gdb.py, jsonpath, que, bootsnap, proxy.rb, kurl, easy_install, premailer, guru, console, revive, idle3.10, s3-meta-sync, memcached_top, sequel, ruby-lsp, corepack, httpclient, parallel_cucumber, term_cdiff, minitest, json-to-dhall, force_clean_accounts.rb, smtpd.py, yri, term_display, python3.9, resque, launchy, nokogiri, foodcritic, pip3, erblint, rufo, cucumber, impl, parallel_spinach, zat, keyify, wsdl2ruby.rb, oauth, changelog, rackup, uuid, golangci-lint, gli, python, dhall-to-json, cap, sdoc, httparty, pydoc3.10, kwalify, byebug, python3.8-config, berks, npm, forking-test-runner, python3.9-config, github-pages, pip2.7, python3-config, tilt, idle3, resque-scheduler, racecarctl, stackprof-gprof2dot.py, tt, convert_to_should_syntax, term_mandel, gofmt, pip2, turn, rdebug-ide, r509, brakeman, dhall-docs, normalizer, mtest, idle3.11, _guard-core, wheel, resque-pool, python3.11-gdb.py, multigem, guard, unit_diff, update_rubygems, srb-rbi, gitlab, cucumber-tag-expressions, rubocop, dhall-to-yaml, gotestsum, erubis, stackprof, sprockets, countloc, python3.10-config, reminder, yaml-to-dhall, stree, sass, r509-parse, agrep, racc2y, serverspec-init, rbprettier, thor, rspec, sass-convert, gotags, goimports, chef-zero, socksify_ruby, shoryuken, minitest_bisect, aruba, dhall-to-toml, rbtrace, pip, parallel_test, tailwindcss, code_owners, 2to3, ruby_parse, pry-remote, blackd, html_tokenizer, ffi-yajl-bench, spoom, toml-to-dhall, term_decolor, editorconfig, rrule, setupkindlerb, aws-v3.rb, private_gem, unicorn_rails, dhall-lsp-server, coderay, spring, listen, chef-shell, dotenv, knapsack, fasterer, apps_approval, ruby-parse, pyproject-build, idle3.8, 2to3-3.11, markdown_py, rumoji, jmespath.rb, kitchen, slim-lint, code_climate_reek, rails, nrdebug, black, python2.7-gdb.py, pry, gemoji, 2to3-3.9, reverse_markdown, pydoc3.9, pathspec-rb, chef-client, ghp-import, gorename, sneakers, pip3.10, pygmentize, staticcheck, python3.11, statsd-to-stdout

Additional context
May be relevant: #278 #1248

[jdx]

I think this is the second time this has regressed, will be useful to put an e2e test around it