Wrap MillBuildRootModule#scriptSourcesPaths in BuildCtx.watchValue (#5954)

This ensures that if you add new `package.mill` files in subfolders,
they get picked up correctly. Previously they may get missed if the
`MillBuildRootModule` does not get re-instantiated (e.g. this happens if
you define a `mill-build/build.mill` meta-build file)

We don't want to just do a `Task.Source(BuildCtx.workspaceRoot)` because
that seems to cause issues, presumably due to trying to hash the entire
project (including `out/` folder) which is slow and expensive

This also lets us clean up some logic in `CodeGen`, replacing
`os.write.over`s with `os.write`s since we can avoid returning duplicate
entries from `walkBuildFiles`

Tested manually

---------

Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>

Author: lihaoyi

runner/meta/src/mill/meta/MillBuildRootModule.scala

@@ -41,10 +41,12 @@ trait MillBuildRootModule()(using
 
   override def scalaVersion: T[String] = BuildInfo.scalaVersion
 
-  val scriptSourcesPaths = BuildCtx.withFilesystemCheckerDisabled {
-    FileImportGraph
-      .walkBuildFiles(rootModuleInfo.projectRoot / os.up, rootModuleInfo.output)
-      .sorted // Ensure ordering is deterministic
+  val scriptSourcesPaths = BuildCtx.watchValue {
+    BuildCtx.withFilesystemCheckerDisabled {
+      FileImportGraph
+        .walkBuildFiles(rootModuleInfo.projectRoot / os.up, rootModuleInfo.output)
+        .sorted // Ensure ordering is deterministic
+    }
   }
 
   /**