New versions of chrome include NaCl with debug stub support. If --enable-nacl-debug switch is passed to chrome or -g switch is passed to sel_ldr, all NaCl applications start with the debug stub enabled. The debug stub stops untrusted code at the first instruction inside the IRT and listens on a TCP port of localhost network interface (4014 currently) for incoming connection from nacl-gdb. When nacl-gdb connects to the debug stub, they talk with each other using RSP protocol. Since remote debugging does not need to use OS-specific debugging functions, we need only one version of nacl-gdb for both 32 and 64-bit debugging. Moreover, if one forwards port to a remote machine, it is possible to use nacl-gdb for one OS to debug NaCl application on a different OS. All the differences between OSes are abstracted away by debug stub.
The debugger is included in the latest version of NaCl SDK. It is located in nacl_sdk/pepper_canary/toolchain/linux_x86_glibc/bin/x86_64-nacl-gdb on Linux, nacl_sdk/pepper_canary/toolchain/win_x86_glibc/bin/x86_64-nacl-gdb.exe on Windows, etc. Debuggers in *_x86_glibc and *_x86_newlib directories are exactly the same. You can use either one on them. Moreover, unlike the rest of SDK, you can copy debugger to a different folder.
Regarding the pepper and chrome versions, the latest debugger should work with the previous versions of chrome/sel_ldr but new functionality may be missing.
NaCl applications can be launched using two ways in Chrome. You can load unpacked extension on chrome://chrome/extensions/ page (switch on developers mode) and open it. Alternative way is to launch a web server and either launch chrome with --enable-nacl switch or enable NaCl applications outside of Chrome Web Store or chrome://flags/ page (you need to relaunch chrome after that). In order to switch on debug stub support, you need to pass --enable-nacl-debug and --no-sandbox switches to chrome. Create a shell script that launches chrome with these flags. You can also add --user-data-dir=some-path to use a separate profile.
In order to debug NaCl application, you need to launch Chrome and open NaCl application there first. Then run x86_64-nacl-gdb. Enter following commands there. If you have spaces in paths, use quotes and double all slashes (or use backslashes).
(gdb) file c:\nacl_sdk\pepper_canary\examples\hello_world\newlib\Debug\hello_world_x86_64.nexe
(gdb) target remote :4014
Point file command to 64-bit nexe on 64-bit platforms and to 32-bit nexe on 32-bit platforms. Then you can use all normal gdb commands.
Debugging glibc applications is harder. You need to use following commands.
If you launched NaCl as unpacked chrome extension or from local http server, you already have the NaCl manifest file which you should use here. If you launched NaCl from an external http server, you need to download *.nmf, *.nexe and *.so files of the NaCl application and place them in the same directory structure that is used on the server (*.nmf file uses relative paths to reference main executable and libraries). Then point nacl-manifest command to the downloaded *.nmf file.
You can additionally load IRT symbols. This helps to understand what application is doing when it is stopped inside NaCl syscall.
Debugging command line NaCl applications is enabled by passing -g switch to sel_ldr. Newlib debugging is the same, glibc debugging requires creating an artificial manifest. You need to reference runnable-ld.so, main executable and all *.so libraries using relative paths from manifest file. If you want to load IRT symbols, use nacl-irt command with the same IRT that is passed to sel_ldr using -B switch.