Annotate visible/hidden paths when all-layers scope

[wagoodman]

#3138 added the concept of annotating locations raised up from a file.Resolver with visible=true or visible=false for any location returned so we can discover packages which have been deleted in higher layers or are otherwise hidden. That PR added a new file.Resolver to take advantage of this new capability, this PR extends these kinds of annotations to the all-layers file resolver (there are no other file resolvers this makes sense to also apply this to).

Here's an example of the changes for a single package in an alpine image where multiple apk add commands were performed each in their own RUN line in the Dockerfile:

$ syft myimage:latest -s all-layers | jq '.artifacts[] | select(.name == "alpine-release").locations'

[
  {
    "path": "/lib/apk/db/installed",
    "layerID": "sha256:02b7b5e2cb1b34e0ed386a34b364f52eaf770e524e120055bdd642e104dce1cd",
    "accessPath": "/lib/apk/db/installed",
    "annotations": {
      "evidence": "primary",
      "visible": "false"
    }
  },
  {
    "path": "/lib/apk/db/installed",
    "layerID": "sha256:a16e98724c05975ee8c40d8fe389c3481373d34ab20a1cf52ea2accc43f71f4c",
    "accessPath": "/lib/apk/db/installed",
    "annotations": {
      "evidence": "primary",
      "visible": "false"
    }
  },
  {
    "path": "/lib/apk/db/installed",
    "layerID": "sha256:eeb7e34dc34ae12fe9df0056d36f9620970ed15c30271462be4dffdef4fc69d2",
    "accessPath": "/lib/apk/db/installed",
    "annotations": {
      "evidence": "primary",
      "visible": "true"
    }
  },
  {
    "path": "/lib/apk/db/installed",
    "layerID": "sha256:ff1223b81bbf3c1c3ffc402947f2a9dfdcf789f9c6acdd36a9d9e60e7c650aa8",
    "accessPath": "/lib/apk/db/installed",
    "annotations": {
      "evidence": "primary",
      "visible": "false"
    }
  }
]

Follow-up to #3138

This does not "fix" #1818 as that issue describes adding an indication on the package and not constituent locations on the package like done in this PR.

Type of change

• New feature (non-breaking change which adds functionality)

Checklist

• I have added unit tests that cover changed behavior
• I have tested my code in common scenarios and confirmed there are no regressions
• I have added comments to my code, particularly in hard-to-understand sections