Remove empty categories after auto-created entity cleanup and add deployment convergence tests

[alexandraminca]

This PR removes empty category keys left behind after auto-created entity cleanup.
After auto-created entities are removed, some category keys, such as pylon, can remain in the configuration even though they no longer contain any entries. The added check removes these category keys when they become empty.
Also adds deployment convergence tests in src-tests/test/deployment/convergence,
testing combinations of XML and CLI configuration:

• Test 1a: node and pylon in XML, agents added via CLI (automatic porting)
• Test 1b: node and pylon in XML, agents added via CLI with explicit in-context-of
• Test 2: node in CLI, pylon and agents in XML with in-context-of
• Test 3: full deployment in XML, additional parameters through CLI

[alexandraminca]

Tested deployment convergence between XML and CLI configuration in src-tests/test/deployment/convergence.

• Boot1a: node and pylon in XML, agents added via CLI -- agents are automatically ported to the pylon.
• Boot1b: node and pylon in XML, agents added via CLI with explicit in-context-of -- agents are correctly placed in the specified pylon.
• Boot2: node in CLI, pylon and agents in XML with in-context-of at pylon level -- the pylon and agents are correctly placed under the CLI-defined node.
• Boot3: full deployment in XML (2 nodes with 2 agents each), additional parameters via CLI for the same agents -- does not work; the framework creates duplicate agent instances instead of merging the configurations, so the CLI parameters are not applied to the XML agents.