Improve VSCode support: update developer manual and fix Eclipse nesting errors

[HenryXi1]

This PR improves support for using VSCode with the Checker Framework.

Changes included:

1. Update developer manual:

   • Instruct VSCode users to run ./gradlew eclipse instead of ./gradle weclipse classpath.
   • Ensures correct Eclipse project and classpath configuration.

2. Fix Eclipse nesting errors:

   • Remove bare 'src/main' entries in build.gradle that cause Eclipse to report nesting errors.
   • Ensures source folders are properly recognized and avoids build errors.

[wmdietl]

Thanks for the improvement!

Do you see the CI error messages?
If not, the misc failure is:

+ git diff --exit-code docs/manual/contributors.tex
diff --git a/docs/manual/contributors.tex b/docs/manual/contributors.tex
index ed211a6a4..83ccd0c90 100644
--- a/docs/manual/contributors.tex
+++ b/docs/manual/contributors.tex
@@ -51,6 +51,7 @@ Haifeng Shi,
 Hamed Taghani,
 Hannes Greule,
 Heath Borders,
+Henry Xi,
 Ivory Wang,
 Jakub Vr\'ana,
 James Yoo,
+ set +x
docs/manual/contributors.tex is not up to date.
If the above suggestion is appropriate, run: make -C docs/manual contributors.tex
If the suggestion contains a username rather than a human name, then do all the following:
  * Update your git configuration by running:  git config --global user.name "YOURFULLNAME"
  * Add your name to your GitHub account profile at https://github.com/settings/profile
  * Make a pull request to add your GitHub ID to
    https://github.com/eisop-plume-lib/git-scripts/blob/master/git-authors.sed
    and remake contributors.tex after that pull request is merged.