Overlay databases: use --overlay-changes

Support diff-informed queries under Default Setup

This commit changes overlay database creation to use the
--overlay-changes flag. It also impleme...

build: sync some utility just instructions I had locally

Co-authored-by: Andrew Eisenberg <aeisenberg@github.com>

Co-authored-by: Andrew Eisenberg <aeisenberg@github.com>

Mergeback v3.28.12 refs/heads/releases/v3 into main

Merge main into releases/v3

Update default bundle to 2.20.7

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

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

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

...

Fix dependabot errors

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

git-utils: deleted unused functions

Minimally remove micromatch

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

Basic support for overlay databases

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

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

...

Bumps the npm group with 3 updates: [@eslint/js](https://github.com/eslint/eslint/tree/HEAD/pack...

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

When a user specifies "cleanup-level: overlay", it suggests that the
user wishes to preserve the...

This commit adds a OverlayDatabaseMode parameter to
databaseInitCluster(). The parameter control...

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

Merge main into releases/v3

Update default bundle to 2.20.6

adjust string for handling rate limit error

Update supported GitHub Enterprise Server versions

Use embedded `actions` extractor only for old CLI versions

build(deps): bump the npm group with 9 updates

build(deps): bump actions/create-github-app-token from 1.11.5 to 1.11.6 in the actions group

Bumps the actions group with 1 update: [actions/create-github-app-token](https://github.com/acti...

Bumps the npm group with 9 updates:

| Package | From | To |
| --- | --- | --- |
| [@actions/cac...

Add some more configuration errors

Do some just+pre-commit tweaking

Warn about small amounts of MB, not GB

The number of GB is at most 2, and can be tiny. MB gives a more
comprehensible range of values.

PR Checks: use semantic versioning for `create-github-app-token`

Fix code injection warnings in `check-codescanning-config` internal Action

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

`runner.temp` is not user-controlled but we replace it with `$RUNNER_TEMP` in any case.

Unify `token` description for `resolve-environment`, `start-proxy`, and `upload-sarif`

Mergeback v3.28.10 refs/heads/releases/v3 into main

Merge main into releases/v3

Support rust analysis

Update default bundle to 2.20.5