Mergeback v3.28.11 refs/heads/releases/v3 into main

When a user specifies "cleanup-level: overlay", it suggests that the
user wishes to preserve the evaluation cache for future use. So in this
case we should not set --expect-discarded-cache when running queries.

Bumps the npm group with 3 updates: [@eslint/js](https://github.com/eslint/eslint/tree/HEAD/packages/js), [@typescript-eslint/eslint-plugin](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/eslint-plugin) and [@typescript-eslint/parser](https://github.com/typescript-eslint/typescript-eslint/tree/HEAD/packages/parser).


Updates `@eslint/js` from 9.21.0 to 9.22.0
- [Release notes](https://github.com/eslint/eslint/releases)
- [Changelog](https://github.com/eslint/eslint/blob/main/CHANGELOG.md)
- [Commits](https://github.com/eslint/eslint/commits/v9.22.0/packages/js)

Updates `@typescript-eslint/eslint-plugin` from 8.26.0 to 8.26.1
- [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases)
- [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/eslint-plugin/CHANGELOG.md)
- [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.26.1/packages/eslint-plugin)

Updates `@typescript-eslint/parser` from 8.26.0 to 8.26.1
- [Release notes](https://github.com/typescript-eslint/typescript-eslint/releases)
- [Changelog](https://github.com/typescript-eslint/typescript-eslint/blob/main/packages/parser/CHANGELOG.md)
- [Commits](https://github.com/typescript-eslint/typescript-eslint/commits/v8.26.1/packages/parser)

---
updated-dependencies:
- dependency-name: "@eslint/js"
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: npm
- dependency-name: "@typescript-eslint/eslint-plugin"
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: npm
- dependency-name: "@typescript-eslint/parser"
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: npm
...

Signed-off-by: dependabot[bot] <support@github.com>

Bumps the actions group with 1 update: [ruby/setup-ruby](https://github.com/ruby/setup-ruby).


Updates `ruby/setup-ruby` from 1.221.0 to 1.222.0
- [Release notes](https://github.com/ruby/setup-ruby/releases)
- [Changelog](https://github.com/ruby/setup-ruby/blob/master/release.rb)
- [Commits](ruby/setup-ruby@32110d4...277ba2a)

---
updated-dependencies:
- dependency-name: ruby/setup-ruby
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>

…0c3752

build(deps-dev): bump the npm group with 3 updates

This commit adds a OverlayDatabaseMode parameter to
databaseInitCluster(). The parameter controls the "codeql database init"
flags concerning overlay database creation.

There is no behavior change in this commit because we always pass
OverlayDatabaseMode.None to databaseInitCluster(). That will change in
the next commit.

This commit adds support for creating overlay-base and overlay
databases, controlled via the CODEQL_OVERLAY_DATABASE_MODE environment
variable.

Basic support for overlay databases

…s-96d25c356e

build(deps): bump ruby/setup-ruby from 1.221.0 to 1.222.0 in the actions group

Minimally remove micromatch

git-utils: deleted unused functions

I explicitly had to downgrade "@octokit/plugin-retry" to "^6.0.0". Other
dependencies were upgraded.

Fix dependabot errors

Bumps the actions group with 1 update: [ruby/setup-ruby](https://github.com/ruby/setup-ruby).


Updates `ruby/setup-ruby` from 1.222.0 to 1.226.0
- [Release notes](https://github.com/ruby/setup-ruby/releases)
- [Changelog](https://github.com/ruby/setup-ruby/blob/master/release.rb)
- [Commits](ruby/setup-ruby@277ba2a...922ebc4)

---
updated-dependencies:
- dependency-name: ruby/setup-ruby
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>

…s-c2c311daa1

build(deps): bump ruby/setup-ruby from 1.222.0 to 1.226.0 in the actions group

…dless

Set and cache dependency directory for Java `build-mode: none`