Add support for configuring knot in pyproject.toml files (#15493)

## Summary

This PR adds support for configuring Red Knot in the `tool.knot` section
of the project's
`pyproject.toml` section. Options specified on the CLI precede the
options in the configuration file.

This PR only supports the `environment` and the `src.root` options for
now.
Other options will be added as separate PRs.

There are also a few concerns that I intentionally ignored as part of
this PR:

* Handling of relative paths: We need to anchor paths relative to the
current working directory (CLI), or the project (`pyproject.toml` or
`knot.toml`)
* Tracking the source of a value. Diagnostics would benefit from knowing
from which configuration a value comes so that we can point the user to
the right configuration file (or CLI) if the configuration is invalid.
* Schema generation and there's a lot more; see
https://github.com/astral-sh/ruff/issues/15491

This PR changes the default for first party codes: Our existing default
was to only add the project root. Now, Red Knot adds the project root
and `src` (if such a directory exists).

Theoretically, we'd have to add a file watcher event that changes the
first-party search paths if a user later creates a `src` directory. I
think this is pretty uncommon, which is why I ignored the complexity for
now but I can be persuaded to handle it if it's considered important.

Part of https://github.com/astral-sh/ruff/issues/15491

## Test Plan

Existing tests, new file watching test demonstrating that changing the
python version and platform is correctly reflected.

crates/red_knot_python_semantic/src/db.rs

@@ -175,7 +175,7 @@ pub(crate) mod tests {
             db.write_files(self.files)
                 .context("Failed to write test files")?;
 
-            let mut search_paths = SearchPathSettings::new(src_root);
+            let mut search_paths = SearchPathSettings::new(vec![src_root]);
             search_paths.typeshed = self.custom_typeshed;
 
             Program::from_settings(

crates/red_knot_python_semantic/src/module_resolver/resolver.rs

@@ -168,7 +168,7 @@ impl SearchPaths {
 
         let SearchPathSettings {
             extra_paths,
-            src_root,
+            src_roots,
             typeshed,
             site_packages: site_packages_paths,
         } = settings;
@@ -186,8 +186,10 @@ impl SearchPaths {
             static_paths.push(SearchPath::extra(system, path)?);
         }
 
-        tracing::debug!("Adding first-party search path '{src_root}'");
-        static_paths.push(SearchPath::first_party(system, src_root.to_path_buf())?);
+        for src_root in src_roots {
+            tracing::debug!("Adding first-party search path '{src_root}'");
+            static_paths.push(SearchPath::first_party(system, src_root.to_path_buf())?);
+        }
 
         let (typeshed_versions, stdlib_path) = if let Some(typeshed) = typeshed {
             let typeshed = canonicalize(typeshed, system);
@@ -1299,7 +1301,7 @@ mod tests {
                 python_platform: PythonPlatform::default(),
                 search_paths: SearchPathSettings {
                     extra_paths: vec![],
-                    src_root: src.clone(),
+                    src_roots: vec![src.clone()],
                     typeshed: Some(custom_typeshed),
                     site_packages: SitePackages::Known(vec![site_packages]),
                 },
@@ -1805,7 +1807,7 @@ not_a_directory
                 python_platform: PythonPlatform::default(),
                 search_paths: SearchPathSettings {
                     extra_paths: vec![],
-                    src_root: SystemPathBuf::from("/src"),
+                    src_roots: vec![SystemPathBuf::from("/src")],
                     typeshed: None,
                     site_packages: SitePackages::Known(vec![
                         venv_site_packages,

crates/red_knot_python_semantic/src/module_resolver/testing.rs

@@ -237,7 +237,7 @@ impl TestCaseBuilder<MockedTypeshed> {
                 python_platform,
                 search_paths: SearchPathSettings {
                     extra_paths: vec![],
-                    src_root: src.clone(),
+                    src_roots: vec![src.clone()],
                     typeshed: Some(typeshed.clone()),
                     site_packages: SitePackages::Known(vec![site_packages.clone()]),
                 },
@@ -295,7 +295,7 @@ impl TestCaseBuilder<VendoredTypeshed> {
                 python_platform,
                 search_paths: SearchPathSettings {
                     site_packages: SitePackages::Known(vec![site_packages.clone()]),
-                    ..SearchPathSettings::new(src.clone())
+                    ..SearchPathSettings::new(vec![src.clone()])
                 },
             },
         )

crates/red_knot_python_semantic/src/program.rs

@@ -103,7 +103,7 @@ pub struct SearchPathSettings {
     pub extra_paths: Vec<SystemPathBuf>,
 
     /// The root of the project, used for finding first-party modules.
-    pub src_root: SystemPathBuf,
+    pub src_roots: Vec<SystemPathBuf>,
 
     /// Optional path to a "custom typeshed" directory on disk for us to use for standard-library types.
     /// If this is not provided, we will fallback to our vendored typeshed stubs for the stdlib,
@@ -115,9 +115,9 @@ pub struct SearchPathSettings {
 }
 
 impl SearchPathSettings {
-    pub fn new(src_root: SystemPathBuf) -> Self {
+    pub fn new(src_roots: Vec<SystemPathBuf>) -> Self {
         Self {
-            src_root,
+            src_roots,
             extra_paths: vec![],
             typeshed: None,
             site_packages: SitePackages::Known(vec![]),
@@ -126,7 +126,7 @@ impl SearchPathSettings {
 }
 
 #[derive(Debug, Clone, Eq, PartialEq)]
-#[cfg_attr(feature = "serde", derive(serde::Serialize))]
+#[cfg_attr(feature = "serde", derive(serde::Serialize, serde::Deserialize))]
 pub enum SitePackages {
     Derived {
         venv_path: SystemPathBuf,
@@ -134,3 +134,12 @@ pub enum SitePackages {
     /// Resolved site packages paths
     Known(Vec<SystemPathBuf>),
 }
+
+impl SitePackages {
+    pub fn paths(&self) -> &[SystemPathBuf] {
+        match self {
+            SitePackages::Derived { venv_path } => std::slice::from_ref(venv_path),
+            SitePackages::Known(paths) => paths,
+        }
+    }
+}