[VC-35738] Replace logs.Log with logr.Logger in the remaining code

[wallrj]

The aim of this PR is to remove the remaining references to the logs.Log variable and replace them with context derived logr.Logger calls.

I haven't given much thought to the log levels because I think we're going to be removing most of the messages about missing CRDs and permissions errors in another feature.

$ go test ./pkg/datagatherer/k8s/... -v -run TestNoneCache -count 1
=== RUN   TestNoneCache
    cache.go:53: E1107 17:57:50.964580] Cache update failure err="not a cacheResource type: *k8s.notCachable missing metadata/uid field" operation="add"
    cache.go:66: E1107 17:57:50.964680] Cache update failure err="not a cacheResource type: *k8s.notCachable missing metadata/uid field" operation="update"
    cache.go:80: E1107 17:57:50.964689] Cache update failure err="not a cacheResource type: *k8s.notCachable missing metadata/uid field" operation="delete"
--- PASS: TestNoneCache (0.00s)
PASS
ok      github.com/jetstack/preflight/pkg/datagatherer/k8s      0.025s

 ./hack/e2e/test.sh

{
  "ts": 1731002359611.0227,
  "caller": "cache/reflector.go:561",
  "msg": "k8s.io/[email protected]/tools/cache/reflector.go:243: failed to list firefly.venafi.com/v1, Resource=issuers: issuers.firefly.venafi.com is forbidden: User \"system:serviceaccount:venafi:venafi-kubernetes-agent\" cannot list resource \"issuers\" in API group \"firefly.venafi.com\" at the cluster scope",
  "v": 0
}
{
  "ts": 1731002359611.0823,
  "caller": "k8s/dynamic.go:278",
  "msg": "datagatherer informer has failed and is backing off",
  "v": 0,
  "groupVersionResource": "firefly.venafi.com/v1, Resource=issuers",
  "reason": "failed to list firefly.venafi.com/v1, Resource=issuers: issuers.firefly.venafi.com is forbidden: User \"system:serviceaccount:venafi:venafi-kubernetes-agent\" cannot list resource \"issuers\" in API group \"firefly.venafi.com\" at the cluster scope"
}

{
  "ts": 1731002360493.6667,
  "caller": "k8s/dynamic.go:276",
  "msg": "server missing resource for datagatherer",
  "v": 0,
  "groupVersionResource": "networking.istio.io/v1alpha3, Resource=gateways"
}
{
  "ts": 1731002360614.0635,
  "caller": "cache/reflector.go:561",
  "msg": "k8s.io/[email protected]/tools/cache/reflector.go:243: failed to list networking.istio.io/v1alpha3, Resource=virtualservices: the server could not find the requested resource",
  "v": 0
}

[maelvls]

Nit: It says that "it logs an error" but we don't assert that something is actually logged. Without seeing the actual log lines, it's hard to see what the test does.

I don't know if it was worth it, but I've opened a PR on top of yours to improve that: #619.

[maelvls]

All good to me. I haven't tested manually nor run the smoke test on my laptop, but I am confident that nothing will break with these changes.

A small nit that we can deal with later: TestCacheNone talks about logs that should be printed, but doesn't assert these logs. I proposed a quick change to fix that in #619; feel free to merge your PR first, and I'll deal with #619 later on.