fix: Updating settings should not clobber discovered projects

`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

crates/project-model/src/project_json.rs

@@ -66,6 +66,8 @@ pub struct ProjectJson {
     /// e.g. `path/to/sysroot/lib/rustlib/src/rust`
     pub(crate) sysroot_src: Option<AbsPathBuf>,
     project_root: AbsPathBuf,
+    /// The path to the rust-project.json file. May be None if this
+    /// data was generated by the discoverConfig command.
     manifest: Option<ManifestPath>,
     crates: Vec<Crate>,
     /// Configuration for CLI commands.