Update cargo, pip, npm dependencies

[FabijanC]

Usage related changes

None

Development related changes

• Specify cargo dependencies only in the root (workspace) Cargo.toml.
• Remove unused num-integer
• Partly resolves Dependabot alerts.
  • High vulnerabilities in package-lock.json (npm) and requirements.txt (pip).
• Update CONTRIBUTING.md on dependency specifying.

Checklist:

• [x] Checked out the contribution guidelines
• [x] Applied formatting - ./scripts/format.sh
• [x] No linter errors - ./scripts/clippy_check.sh
• [x] No unused dependencies - ./scripts/check_unused_deps.sh
• [x] No spelling errors - ./scripts/check_spelling.sh
• [x] Performed code self-review
• [x] Rebased to the latest commit of the target branch (or merged it into my branch)
• [x] Updated the docs if needed - ./website/README.md
• [x] Linked the issues resolvable by this PR - linking info
• [x] Updated the tests if needed; all passing - execution info