Remove znet-bookkeeping.[h|c] files

[vivien-apple]

Problem

In order to makes it easier to move forward on #3464, I'm trying to extract the parts that are not fully dependent on ZAP.
It should makes it easier to understand the scope of various changes from #3464

This PR is the part of #3464 that removes znet-bookkeeping.h and net-bookkeeping.c files from the gen/ folders.

Summary of Changes

• Delete znet-bookeeping.h and net-bookkeeping.c files from the various gen/ folders.
• Update the name of some methods in src/app/util/af-main-common.c and src/app/util/util.cpp with the Callback prefix. Basically the znet-bookkeeping methods were just calling those
• emAfInit -> emberAfInit. emAfInit uses to call emberAfMainInitCallback and emberAfInit and emberAfMainInitCallback was an empty stub.

[github-actions]

Size increase report for "esp32-example-build" from 3a1312d

File	Section	File	VM
chip-wifi-echo.elf	.flash.text	-180	-180

Full report output

BLOAT REPORT

Files found only in the build output:
    report.csv

Comparing ./master_artifact/chip-wifi-echo.elf and ./pull_artifact/chip-wifi-echo.elf:

sections,vmsize,filesize
.shstrtab,0,1
.debug_ranges,0,-88
.debug_aranges,0,-104
.symtab,0,-128
.flash.text,-180,-180
.strtab,0,-181
.debug_frame,0,-256
.debug_loc,0,-313
.debug_str,0,-424
.debug_abbrev,0,-576
.debug_line,0,-1520
.debug_info,0,-5083

[github-actions]

Size increase report for "nrfconnect-example-build" from 3a1312d

File	Section	File	VM
chip-lock.elf	shell_root_cmds_sections	-12	-12
chip-lock.elf	text	-68	-68
chip-lighting.elf	shell_root_cmds_sections	4	4
chip-lighting.elf	text	-68	-68

Full report output

BLOAT REPORT

Files found only in the build output:
    report.csv

Comparing ./master_artifact/chip-shell.elf and ./pull_artifact/chip-shell.elf:

sections,vmsize,filesize

Comparing ./master_artifact/chip-lock.elf and ./pull_artifact/chip-lock.elf:

sections,vmsize,filesize
.shstrtab,0,1
shell_root_cmds_sections,-12,-12
text,-68,-68
.debug_ranges,0,-88
.debug_aranges,0,-104
.strtab,0,-161
.symtab,0,-208
.debug_frame,0,-244
.debug_str,0,-428
.debug_loc,0,-556
.debug_abbrev,0,-607
.debug_line,0,-1127
.debug_info,0,-5110

Comparing ./master_artifact/chip-lighting.elf and ./pull_artifact/chip-lighting.elf:

sections,vmsize,filesize
shell_root_cmds_sections,4,4
.shstrtab,0,-3
text,-68,-68
.debug_ranges,0,-88
.debug_aranges,0,-104
.strtab,0,-161
.symtab,0,-208
.debug_frame,0,-244
.debug_str,0,-342
.debug_loc,0,-558
.debug_abbrev,0,-607
.debug_line,0,-1147
.debug_info,0,-5110

[vivien-apple]

I pushed an update that removes the changes to the nrf5 examples since #3605 has removed them.

[rwalker-apple]

@jelderton @saurabhst @BroderickCarlin @hawk248 ?