docs: fix broken table-of-contents links in docs/README.md

[avneetbansal-aws]

Several links in docs/README.md point to flat paths, but those pages were reorganized into subdirectories, so the links 404 on GitHub. This corrects the moved-file links under working-with-projects (create-projects, project-configuration, working-with-images), updates the two vulnerability-scanning links that were renamed from image to artifact (scan-individual-artifact.md, scan-all-artifacts.md), and fixes the E2E guide link whose filename switched from underscores to hyphens (e2e-api-python-based-scripting-guide.md).

Three more links still look broken, but the intended target is not obvious, so I left them out and am happy to follow your preferred targets:

• working-with-projects/managing-helm-charts.md: the chart museum was replaced by OCI, so the likely replacement is working-with-projects/working-with-oci/working-with-helm-oci-charts.md. That is a content decision rather than a pure link fix.
• administration/upgrade/upgrade-migrate-data.md: the upgrade section was restructured into _index.md, helm-upgrade.md, roll-back-upgrade.md, and upgrade-test.md. Pointing at _index.md would work if that matches your intent.
• build-customize-contribute/configure-swagger.md: no matching page exists in that directory (only swagger.yaml), so I was not sure what the link should resolve to.

Note this README is labelled as the Harbor 2.1.x table of contents; if it is considered legacy I am glad to adjust or drop the change as you see fit.

[chlins]

lgtm