chore(deps): update and fix dependency tree

Makefile

apps/docs/package.json

apps/web/package.json

apps/web/src/components/onboarding/onboarding.tsx

libs/config/package.json

libs/shared/lib/components/Resizable.tsx

libs/shared/lib/data-access/store/mlSlice.ts

libs/shared/lib/data-access/store/visualizationSlice.ts

libs/shared/lib/querybuilder/model/graphology/utils.ts

libs/shared/lib/vis/nodelink/components/NLPixi.tsx

libs/shared/package.json

libs/storybook/package.json

libs/workspace/eslint-config-custom/package.json

package.json

pnpm-lock.yaml