ci: group updates to decrease the amount of Dependabot PRs

[triceo]

Description of the change

Description here

Checklist

Development

• The changes have been covered with tests, if necessary.
• You have a green build, with the exception of the flaky tests.
• UI and JS files are fully tested, the user interface works for all modules affected by your changes (e.g., solve and analyze buttons).
• The network calls work for all modules affected by your changes (e.g., solving a problem).
• The console messages are validated for all modules affected by your changes.

Code Review

• This pull request includes an explanatory title and description.
• The GitHub issue is linked.
• At least one other engineer has approved the changes.
• After PR is merged, inform the reporter.

[Copilot]

Pull Request Overview

This PR adjusts the Dependabot update schedule and consolidates multiple dependency updates into single pull requests to reduce noise.

• Changed update time from '05:00' to '03:00' for all ecosystems
• Added a groups section under each package ecosystem to bundle all updates into a single PR

Comments suppressed due to low confidence (2)

.github/dependabot.yml:12

• The groups configuration is repeated for each ecosystem block. Consider using YAML anchors or a shared snippet to DRY these definitions and simplify future maintenance.

    groups:

.github/dependabot.yml:13

• [nitpick] The group name all is very generic. Consider a more descriptive name like all-dependencies to clarify its purpose and prevent naming collisions down the road.

      all: # Group all updates together.