The only case where you have to resort to writing binary code manually
is when the assembler cannot output the desired code for some reason.
If I recall correctly, there is only one such case in the HelenOS
sources:

http://trac.helenos.org/browser/mainline/kernel/arch/mips32/include/debug.h?rev=mainline%2C1446.3.1

Here they manually encode the opcodes of five special debugging
instructions for the MSIM MIPS simulator (these instructions are not
part of the standard MIPS ISA, thus the assembler does not know them).

What are the other problems that the Assembly does not solve?

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