refactor(source): move every implementation into its module directory

- 36 files move into the module whose AGENTS.md already claimed them:
  Engine/, Synth/, Modulation/, Params/, Plugin/, GUI/, EffectUnits/, Resources/
- Source/engine, modulation, params, plugin and synth become Engine,
  Modulation, Params, Plugin and Synth, matching the directories that already
  hold code
- ExactCompare.h stays at the Source/ root as the one shared header
- SERUMALT_INCLUDE_DIRS adds one include directory per module, so the 31
  parent-relative includes become plain names with no path prefix
- the module AGENTS.md files list owned files instead of describing a move
  that had not happened, and README.md and AGENTS.md describe the real tree

Verified: the harness passes CTest, the Linux VST3 and Standalone link, the
Windows cross-build passes its module checks, each configure exposes only its
own targets, no first-party warning line appears, and the generated Windows
manifest is unchanged.

Source/Presets/FactoryPresets.h

@@ -1,8 +1,8 @@
 #pragma once
 
 #include <JuceHeader.h>
-#include "../Params.h"
-#include "../ModulationMatrix.h"
+#include "Params.h"
+#include "ModulationMatrix.h"
 
 namespace serum
 {