@gerritv Sorry, just re-read your msg and you already have the .ino in correct place.
Are you certain there is no .ino outside the src directory? Are you using the development version of the libraries as well as the example from it?
I recently changed my MySensors lib directory to be direct from Git development branch so the platformio lines are a bit different now (but same idea)
[platformio]
lib_dir = ../MySensorsLib/libraries
[env:nodemcuv2]
platform = espressif
framework = arduino
board = nodemcuv2
build_flags = -I../MySensorsLib/libraries/MySensors
lib_ignore = MySensors
targets = upload
Example output from my recent build:
1>------ Build started: Project: GW-ESP8266, Configuration: Debug Win32 ------
1> [04/07/16 11:47:31] Processing nodemcuv2 (framework: arduino, build_flags: -I../MySensorsLib/libraries/MySensors, lib_ignore: MySensors, platform: espressif, board: nodemcuv2, targets: upload)
1>
1> xtensa-lx106-elf-g++ -o .pioenvs\nodemcuv2\src\tmp_ino_to.o -c -fno-rtti -fno-exceptions -std=c++11 -Os -mlongcalls -mtext-section-literals -falign-functions=4 -ffunction-sections -fdata-sections -MMD -DF_CPU=80000000L -D__ets__ -DICACHE_FLASH -DESP8266 -DARDUINO_ARCH_ESP8266 -DARDUINO_ESP8266_ESP12 -DARDUINO=20100 -DPLATFORMIO=020805 -U__STRICT_ANSI__ -IC:\Users\gerrit\.platformio\packages\framework-arduinoespressif\tools\sdk\include "-IC:\Users\gerrit\Documents\My Projects\SensorNet\MySensorsLib\libraries\MySensors" -I.pioenvs\nodemcuv2\FrameworkArduino -I.pioenvs\nodemcuv2\FrameworkArduinoVariant -I.pioenvs\nodemcuv2\EEPROM -I.pioenvs\nodemcuv2\SPI -I.pioenvs\nodemcuv2\ESP8266WiFi src\tmp_ino_to.cpp
1> xtensa-lx106-elf-g++ -o .pioenvs\nodemcuv2\firmware.elf -Os -nostdlib -Wl,--no-check-sections -u call_user_start -Wl,-static -Wl,--gc-sections -Wl,-wrap,system_restart_local -Wl,-wrap,register_chipv6_phy -Wl,-T"esp8266.flash.4m1m.ld" .pioenvs\nodemcuv2\src\tmp_ino_to.o -LC:\Users\gerrit\.platformio\packages\framework-arduinoespressif\tools\sdk\lib -LC:\Users\gerrit\.platformio\packages\ldscripts -L.pioenvs\nodemcuv2 -Wl,--start-group .pioenvs\nodemcuv2\libFrameworkArduinoVariant.a .pioenvs\nodemcuv2\libFrameworkArduino.a -lmesh -lwpa2 -lsmartconfig -lpp -lmain -lwpa -llwip -lnet80211 -lwps -lcrypto -lphy -lhal -laxtls -lgcc -lm .pioenvs\nodemcuv2\libEEPROM.a .pioenvs\nodemcuv2\libSPI.a .pioenvs\nodemcuv2\libESP8266WiFi.a -Wl,--end-group
1> "C:\Users\gerrit\.platformio\packages\tool-esptool\esptool" -eo "C:\Users\gerrit\.platformio\packages\framework-arduinoespressif\bootloaders\eboot\eboot.elf" -bo .pioenvs\nodemcuv2\firmware.bin -bm dio -bf 40 -bz 4M -bs .text -bp 4096 -ec -eo .pioenvs\nodemcuv2\firmware.elf -bs .irom0.text -bs .text -bs .data -bs .rodata -bc -ec
1> <lambda>(["upload"], [".pioenvs\nodemcuv2\firmware.bin"])
1> Auto-detected UPLOAD_PORT/DISK: COM6
1> "C:\Users\gerrit\.platformio\packages\tool-esptool\esptool" -vv -cd nodemcu -cb 115200 -cp COM6 -cf .pioenvs\nodemcuv2\firmware.bin
1> esptool v0.4.8 - (c) 2014 Ch. Klippel <ck@atelier-klippel.de>
1> setting board to nodemcu
1> setting baudrate from 115200 to 115200
1> setting port from COM1 to COM6```