fix: external tools producing duplicate keys

[miki725]

• Followed the steps in the contributor's guide: https://crashoverride.com/docs/other/contributing#filing-the-pull-request
• PR title uses semantic commit messages
• Filled out the template to a useful degree
• Updated CHANGELOG.md if necessary

Issue

SBOM key was reported both on report and chalk mark level:

{
  "_CHALKS": {"SBOM": {...}},
  "SBOM": {...}
}

Description

Some tools work on context directories (e.g. sbom) and for non-fs artifacts (e.g. docker image), sbom tool would run both during host chalk time as well as artifact chalk time collections. As both would collect its output for the same path input, it would produce duplicate output in both report and chalk mark levels.

Now any tool can run at most once and any future attempts for the same path are skipped which removes duplicate keys.

Testing

➜ make tests args="test_plugins.py::test_syft_docker --logs"