I have been fighting this same problem for ages.

One thing I have noticed, if changes are made in a class then usually (but not always) the deep search is very quick as caching seems to work and I get "Using previously compiled file:" messages.

However ANY change to the project .ino file causes a full deep search and rebuild to occur and it´s time to make a coffee while I wait.

I have emailed the outputs.

I have tried not using deep search but without success. 
Unless there is a way to manually add include paths then it just fails almost immediately - for example ArduinoOTA.h includes WIFIUdp.h which is not found so build fails.

This is exhibited in the following case even with deep search enabled.
When including a library it automatically gets included in the .ino file.

if I don´t need the library in the .ino code but in a class so I add the header where it´s actually needed (in the cpp) and delete the header from the ino, when I compile I get a file not found error. If the header is in the ino it compiles correctly.

Digging a bit more I have found that if the header is included in the class header then it compiles as long as the class is included in the ino. It also shows up in the deep search output. If it is in the cpp file then it doesn´t.

I´m guessing the first thing that happens is a trawl of all the linked header files to extract the included headers. These are then used in deep search. A header in a cpp file isn´t included. I assume the idea behind deep search is to avoid having to add include paths manually.

I have tested this with the TimeLib library. Adding the full path as an include in my class cpp file (I also have to add the cpp as well) removes the library from deep search and the project compiles.

#include <C:\Arduino\libraries\Time\TimeLib.h>
#include <C:\Arduino\libraries\Time\Time.cpp>


So could one (even short term?) solution to this be a method for manually adding a search path to the compiler includes path in the board.txt for example?