The doc mentions the page "Administer => System Settings => Cleanup Caches and Update Paths" as a way to clear caches. This is half-true: it does clear `templates_c` and the `civicrm_cache` table, but there are other things that it doesn't touch. (Compare `CRM_Admin_form_Setting_UpdateConfigBackend::postProcess` with the `CRM_Core_Invoke::rebuildMenuAndCaches`.)

IMHO, `UpdateConfigBackend::postProcess` should be patched to just do a general system flush (`civicrm_api3('System', 'flush', array())`) -- but (for now) the page is misleading and we shouldn't direct people there.

- Add details about how to do query logging to a table instead of a
  file.
- Put instructions into steps in chronological order.

 * Cleanup syntax of `define()`s. Add another.
 * Add `angularDebug=1` / `crm-ui-debug`.
 * Add more ways to clear the cache.
 * Consolidate discussions of xdebug (for all other/undocumented/external)

https://wiki.civicrm.org/confluence/display/CRMDOC/Debugging+for+developers