`refresh_data` reloaded the four data lists and updated the tab labels
plus status bar, but only called `populate_agents` and `populate_skills`.
Rules were not repopulated (though `populate_rules` already existed) and
Commands had no reusable populate helper at all — initial population was
inlined in `create_commands_tab`. After clicking "Refresh Data" the tab
counts changed but the Rules and Commands treeviews still showed pre-
refresh rows, and the "Data refreshed successfully!" popup silently lied.
Extract the commands-tree insertion into `populate_commands` mirroring
`populate_agents`/`populate_rules`, then call both `populate_commands`
and `populate_rules` from `refresh_data`.
Fixes#2513
