That makes sense -> conclusion - no need to edit project.properties and no need for .particle.include and .particle.ignore.
What had thrown me was that when I ran "particle compile photon", I got lines like this:
lib/Adafruit_SSD1306/examples/ssd1306_128x64_i2c/ssd1306_128x64_i2c.ino
lib/Adafruit_SSD1306/examples/ssd1306_128x64_spi/ssd1306_128x64_spi.ino
lib/Adafruit_SSD1306/examples/surfsoon-oled/surfsoon-oled.ino
ie it looked like the examples sub-dir under a library was being compiled, but from what you have indicated (and the evidence now that I look at it), it is not (good).
Same thing with the following. I have a work in progress sub-dir "wip" at the top which gets pushed to the repo, but I don't want it compiled per se, but get lines like this with the compile:
wip/anothersubdir/another.cpp
I will call this case closed (noting that I did not open this case).
Cheers!