feat(conf): default --entry-layer to kernel (#4076)

The node binary is most often run as a transport-only service/fleet node, so
`logosdeliverynode` no longer mounts the messaging client and reliable channel
manager unless asked. Protocol flags are unchanged in the default case: the
individual CLI defaults already match what `applyMode(Core)` was setting.

Only the CLI default moves. `LogosDelivery.new(entryLayer = ...)` and
`parseLogosDeliveryConf` keep defaulting to `channels`, so the Nim and C library
entry points are unaffected. `MessagingClientConf.toWakuNodeConf` pins
`entryLayer = channels` for the same reason it already pins `mode`: a conf
derived from a messaging config is by construction not kernel-only.

`LogosDeliveryConf.init` now honours `entryLayer == kernel` instead of always
mounting the messaging layer, so the layer it records and the layers it mounts
agree. Doc comments follow the code: `mode`/`preset` shape the kernel conf for
every layer, `kernel` included, and `init(kernelConf)` stays the raw entry.

Co-authored-by: NagyZoltanPeter <113987313+NagyZoltanPeter@users.noreply.github.com>
Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>

examples/api_example/api_example.nim

@@ -63,6 +63,9 @@ when isMainModule:
     echo "Failed to create default config: ", error
     quit(QuitFailure)
 
+  # The CLI default is kernel-only; this example drives the messaging API.
+  conf.entryLayer = EntryLayer.channels
+
   if args.ethRpcEndpoint == "":
     # Create a basic configuration for the Waku node
     # No RLN as we don't have an ETH RPC Endpoint