[docs] Update paths and version of Doxygen.in to fix warnings.

[turon]

Problem

The current Doxyfile.in has a few issues:

1. Warning advising to update the Doxyfile to the latest version by running doxygen -u on it.
2. Many missing paths to new source.

Summary of Changes

Run doxygen -u on the config and add new paths such as src/app, src/lib/shell, and src/transport, etc.

[chip-bot]

Size increase report for "Build Examples [nRF]"

File	Section	File	VM

Full report output

Bloat report for job 'Build Examples [nRF]'

Files found only in the baseline:
    bloat_report.txt

Comparing master_binaries/nrf-build/chip-nrf52840-lock-example.out and example_binaries/nrf-build/chip-nrf52840-lock-example.out:

sections,vmsize,filesize

[chip-bot]

Size increase report for "Build Examples [ESP32]"

File	Section	File	VM
chip-wifi-echo.elf	.flash.text	36	36

Full report output

Bloat report for job 'Build Examples [ESP32]'

Files found only in the baseline:
    bloat_report.txt

Comparing master_binaries/esp32-build/chip-wifi-echo.elf and example_binaries/esp32-build/chip-wifi-echo.elf:

sections,vmsize,filesize
.flash.text,36,36
[Unmapped],0,4

[chip-bot]

Size increase report for "Build Examples [main-build]"

File	Section	File	VM

Full report output

Bloat report for job 'Build Examples [main-build]'

Files found only in the baseline:
    bloat_report.txt

Comparing master_binaries/main-build/chip-standalone-demo.out and example_binaries/main-build/chip-standalone-demo.out:

sections,vmsize,filesize