As taken from 
http://atariage.com/forums/topic/216515-debugging-using-altirra/?p=2827027
<P>
General
<UL>
<LI>   The debugger has built-in help. Use [.help] to get a list of commands 
and [.help command] to get help on a specific command.
<LI>   Essential keyboard shortcuts: F8 (run/stop), F10 (step over), F11 
(step into)
<LI>   In the command line, Up/Down accesses command history, Shift+Up/Down 
scrolls the output portion, and Enter repeats last command with 
continuation.
<LI>   Newer versions of the debugger support tabs; use View > Reset 
Window Layout if you have the old layout, and you should get the new, more 
compact default layout with stacked Registers/Disassembly/History. You can 
manually stack tabs by dragging them and hovering over the center of a 
docking diamond.
<LI>   If you are running Altirra through WINE, reset the font in Debug > 
Options > Font. It's supposed to be a monospace font, but WINE lacks one 
of the standard fonts.
<LI>   The default radix is mixed, which allows bare hex except in an 
expression: 10 = $10 = (16). Use [.base dec] or [.base hex] to force a 
different radix.
<LI>   Create a text file called startup.atdbg in the program dir if you 
have favorite commands you want to run on startup.
</UL>
Assemble/run setup
<UL>
<LI>    If you are using MADS, build labels (-t) and a listing (-l). .lab 
and .lst files with the same name as an .xex will automatically get picked up 
if you start the .xex from the emulator. You really want labels loaded.
<LI>    If you are loading the executable from DOS, use the .loadsym 
command to manually load labels and listings.
<LI>    The /singleinstance command-line switch is very useful as it 
forces reuse of an already running instance of the emulator, regardless of the 
setting in Options. It allows a batch file to build the program and 
automatically launch it in the existing debugger without restarting it, 
keeping history and settings.
<LI>    If you have data files, consider using virtual disk mounting to 
avoid having to constantly rebuild a disk image. This is done through the [F] 
button in the Disk Drive dialog in versions through 2.20, and the right 
arrow drop-menu in 2.30+. The virtual disk driver monitors for file 
changes and will automatically update the virtual disk when a host file 
changes. You can also use the host device (H:) for this, if you are using 
CIO.
<LI>    When using MADS with a listing file loaded, you can automatically 
set conditional breakpoints through comments that begin with ;##ASSERT and 
;##TRACE. Examples: [;##TRACE "dy = %d" db(deltar)] and [;##ASSERT 
dw(oldadr) >= dw(savmsc)]. TRACEs print out info using .printf syntax, and 
ASSERTs stop if the condition is false. These will show up in [bl] output 
if they were picked up correctly.
</UL>
6502 debugging (immediate)
<UL>
<LI>    Use [t] or F11 to step by one instruction, [o] or F10 to step over 
one instruction (skips calls and interrupts), and [g] to continue execution.
<LI>    Use [r] to get your bearings without looking at the Register 
window or to change registers: [r pc $0600].
<LI>    Use [a8] to set aliases to match most Atari800 debugger commands. 
Use [.help a8] to see the mappings from Atari800 commands to Altirra commands.
<LI>    To set a breakpoint, use [bp address]. [bl] lists breakpoints, and 
[bc] clears breakpoints (by index, not address). The index is shown in 
[bl] output or when you set the breakpoint, i.e. "Breakpoint 0 set at 
address $A000." Use [bc *] to clear all breakpoints.
<LI>    To set a data breakpoint on an address, use [ba]. For instance, 
[ba r vcount] will set a read breakpoint on VCOUNT, and [ba w d300 L100] will 
break on any writes into the PIA region.
<LI>    To set a conditional breakpoint, use [bx "condition"]. This can be 
either a PC or a data breakpoint: [bx "write=irqen and pc>$c000 and 
(value&8)"] will fire when the OS enables the serial output complete 
interrupt.
<LI>    Breakpoints can automatically execute a list of commands when they 
fire, separated by semicolons. This is most useful in conjunction with the 
.printf command: [bp siov ".printf \"SIO request from $%04X\" (pc); g"]. 
The set tracepoint [bt] command makes this easier in 2.40-test.
<LI>    [k] dumps the call stack, if you want to know what called the 
current routine (or more precisely, where it will return to).
<LI>    To modify memory, use [e]: [e 4000 00 01 03].
<LI>    To display memory, use db (display byte). There are also dw 
(word), dd (doubleword), df (decimal float), da (ATASCII string), and di (INTERNAL 
string). If you only want to view one byte or word, and particularly if 
you want to see decimal, use [? db(address)] or [? dw(address)].
<LI>    [ln] does a lookup from address to symbol.
<LI>    [?] evaluates an expression. Useful for checking out state, and 
very useful when you're bad at math or just need a dec/hex conversion.
<LI>    [.vectors] dumps out a list of OS and CPU vectors.
<LI>    [.bank] and [.pia] show the memory banking and PIA state, 
respectively, and are useful for debugging extended memory usage bugs. 
Extended addressing syntax also allows the debugger to access xmem 
directly even if it isn't banked in: [db x:$8000].
<LI>    [.map] shows the status of all memory layers. It's most useful to 
tell when you've accidentally enabled BASIC or the self-test ROM, or forgot to 
disable a cartridge.
<LI>    When debugging a program that takes over the whole machine, use 
[.unloadsym kerneldb] to unload the OS kernel database symbols so you 
don't see OS symbols where low page zero is reused.
<LI>    Quick-assemble small code fragments with [a address]. Type one 
line of asm at a time and hit Enter alone to end.
<LI>    It's useful to enable System > CPU > Stop on BRK instruction.
</UL>
6502 debugging (deferred)
<UL>
<LI>    Enable instruction-level history (System > CPU > Record 
instruction history). This enables the History debug pane, which is extremely useful 
for telling what happened after the fact. It has a tree-view that 
collapses loops, subroutine calls, and interrupts, making it easier to 
tell what's going on. I spend most of the time in the Console and History 
panes.
<LI>    For monitoring values over a long period of time and that 
correspond to on-screen activity, on-screen watches can be useful: [wb/ww] to watch a 
byte or word by address, and [wc] to clear. For instance, you can watch 
horizontal and vertical position values this way. Note that these only 
update once a frame.
<LI>    Path tracing can be useful to find out what the active regions of 
a program are. It is enabled either in CPU Options or with [.pathrecord on], 
and modified by the other path commands; executed code can be dumped with 
[.pathdump]. Another use for it is to find the exit path that responds to 
an input: use [.pathclear] to reset the path history, let the emulation 
run for a while to capture the loop path, then enable [.pathbreak on] and 
hit the joystick button or START to find out what responds to those 
buttons.
</UL>
6502 optimization
<UL>
<LI>    Profile View (Debug > Profile > Profile View) will show which 
portions of a program are using the most CPU time. Click on a header button to 
re-sort, and double-click on an entry to see annotated disassembly.
<LI>    The History window can also be used to assess performance: right 
click on the entry to a block and select [Set Timestamp Origin], then 
right-click again and select [Timestamp Format > Show Cycles]. Every 
instruction in the history will then show when it relatively started in 
machine cycles. You can also use [Timestamp Format > Show Unhalted Cycles] 
to show how many CPU cycles were taken, ignoring DMA.
</UL>
Audio
<UL>
<LI>    [.pokey] dumps POKEY state.
<LI>    Enable the audio monitor (Audio > Audio Monitor) to visually see 
what POKEY's audio channels are doing.
<LI>    Toggle individual audio channels with Ctrl+Alt+[1-4] to isolate 
squawking channels.
</UL>
BASIC
<UL>
<LI>    [.basic] shows the current BASIC pointers and the memory taken by 
each region.
<LI>    [.basic_vars] dumps out all variables.
<LI>    [.basic_dumpline] dumps out a tokenized BASIC line by address.
<LI>    When running, i.e. not stopped in the debugger, shift+hover over 
an error message will translate the error code.
</UL>
Character I/O (CIO)
<UL>
<LI>    [.tracecio on] will log all calls made to OS CIO, decoding 
parameters for some of them. It's most useful for figuring out what commands a 
program is issuing to DOS.
<LI>    The debug display (Debug > Window > Debug Display) can show you 
what is on the OS screen when your program crashes before ANTIC+GTIA have drawn 
it.
<LI>    [.ciodevs] dumps out all character devices registered in HATABS.
<LI>    [.iocb] dumps out the I/O control blocks.
</UL>
Disk I/O / SIO
<UL>
<LI>    For sector-level access, enable the DISKCMD and HOOKSIO logging 
channels ([lfe diskcmd] / [lfe hooksio]). The debugger will then log which 
sectors are being read, and if regular OS SIO is being used, the SIO patch 
hook will also print out addresses. There are other useful logging 
channels: [lfl] to list.
<LI>    For hardware-level access, use [.traceser on] to get a dump of 
what bytes are going in and out of the serial port registers and whether 
overruns/underruns are happening.
<LI>    [bs sector] will fire a breakpoint when a particular disk 
sector is read.
<LI>    [.sio] dumps out the disk control block (DCB), which contains the 
current SIO request.
<LI>    [.diskdumpsec] will dump out a raw disk sector.
<LI>    You can explore the contents of any mounted DOS 2 or SpartaDOS 
disk by selecting Arrow -> Explore on a drive in the Disk Drives dialog. Files can 
then be dragged out of the Disk Explorer into the host filesystem.
</UL>
Graphics
<UL>
<LI>    The display window will show the current beam position on screen 
as a yellow line, immediately below the beam position.
<LI>    [.antic] dumps ANTIC state, and [.gtia] dumps GTIA state.
<LI>    The go until scanline [gs] command is very useful for debugging 
graphics glitches. Typically I do [gs 240] or so until the glitch appears 
on-screen, then use the History window and the display list history to 
figure out what happened. The [gs] command automatically runs a full frame 
if you give it the vertical position that the beam is already on, so you 
can just spam it by alternating Up/Enter until a broken frame comes up.
<LI>    When execution is stopped, shift+hover over the display window 
will indicate beam position and display list activity for a point on screen.
<LI>    The display list history (.dlhistory) shows what ANTIC has 
executed. 
It's useful for telling whether something is going wrong with the display 
list.
<LI>    Conditional breakpoint expressions can include the horizontal and 
vertical beam position (hpos/vpos), so it's possible to have the debugger 
break when a DLI runs late or at the wrong time: [bx "pc=addr and vpos != 
100"].
<LI>    (2.40-test only) If your display list is glitching out when trying 
HSCROL tricks, enable Debug > Verifier > Abnormal playfield DMA. This will 
cause a break into the debugger when playfield DMA goes haywire when 
HSCROL is hit at the wrong time.
</UL>
Expansion hardware
<UL>
<LI>    VideoBoard XE: [.vbxe] for general status, [.vbxe_bl] to dump a 
blitter command list, [.vbxe_xdl] to dump the extended display list, and 
[.vbxe_traceblits] to log blits.
<LI>    Ultimate1MB: [.ultimate] to dump status, [.ds1305] to dump 
real-time clock status.
<LI>    SIDE: [.ds1305] to dump real-time clock status.
<LI>    MyIDE/SIDE/IDEPlus: [.ide] to dump IDE status, [.ide_dumpsec] to 
dump out a sector, and [.ide_rdsec]/[.ide_wrsec] to do DMA to and from CPU 
memory.
</UL>