`linkedProjects` is owned by the user's configuration, so when users
update this setting, `linkedProjects` is reset. This is problematic when
`linkedProjects` also contains projects discovered with `discoverCommand`.
The buggy behaviour occurred when:
(1) The user configures `discoverCommand` and loads a Rust project.
(2) The user changes any setting in VS Code, so rust-analyzer receives
`workspace/didChangeConfiguration`.
(3) `handle_did_change_configuration` ultimately calls
`Client::apply_change_with_sink()`, which updates `config.user_config`
and discards any items we added in `linkedProjects`.
Instead, separate out `discovered_projects_from_filesystem` and
`discovered_projects_from_command` from user configuration, so user
settings cannot affect any type of discovered project.
This fixes the subtle issue mentioned here:
https://github.com/rust-lang/rust-analyzer/pull/17246#issuecomment-2185259122
3cf28f1fc6