Harness config 1.0.0-alpha.3

1.0.0-alpha.3 updates the v1 proposal to the ordered source-root model and
adds projection introspection for reviewable customization workflows.

Ordered Source Roots

• Replaces legacy single [resources] and [dir] manifest tables with
  ordered [[resources]] and [[dir]] source roots.
• Treats missing configured source roots as empty layers, with later roots
  overriding earlier exact-path outputs and composable leaves merging parts.
• Rejects source/target overlaps and incompatible file/folder projections
  before activation writes.

Tooling And Docs

• Adds harnessc explain <path> for read-only projection introspection.
• Updates harnessc init, docs, package READMEs, skill guidance, and website
  specification content to use array-root examples.
• Documents optional single-developer customization layers such as
  .harness/local/resources and .harness/local/dir as recommendations, not
  standard requirements.