Changing internal NIOS build for DDR IP in Stratix V, without changing tool tree

I have searched for ddr and NIOS and cannot find anything appropriate on the forums.

If someone knows of a similar question/solution, please just let me know.

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I have some changes I'd like to make to the file sequencer.c before it is used *inside* the DDR3 IP in a Stratix V Device.

I'm currently achieving this by changing the file inside the tool tree, but this makes tracking hard.

I'm referring to the file .../13.0sp1/ip/altera/alt_mem_if/altera_mem_if_qseq/software_110/sequencer_c/sequencer.c

My flow at the moment is 3 phases on the command line:

1. to generate all files from QSYS files from the command line using:
   • > qsys-generate system.qsys --synthesis=VERILOG

2. Build the qsf from a TCL script, (exported and modified from quartus).

3. Using quartus_sh and "execute_flow -compile"

After the first step I have the following files: (ignoring the verilog and system verilog files)

$ find  system_ddr3_0* -type f | egrep -v "\.v|\.sv"
system_ddr3_0_p0_parameters.tcl
system_ddr3_0_p0_pin_assignments.tcl
system_ddr3_0_p0_pin_map.tcl
system_ddr3_0_p0.ppf
system_ddr3_0_p0_report_timing_core.tcl
system_ddr3_0_p0_report_timing.tcl
system_ddr3_0_p0.sdc
system_ddr3_0_p0_timing.tcl
system_ddr3_0_s0_AC_ROM.hex
system_ddr3_0_s0_inst_ROM.hex
system_ddr3_0_s0_make_qsys_seq.tcl
system_ddr3_0_s0_sequencer_mem.hex
system_ddr3_0_s0_software/core_debug.h
system_ddr3_0_s0_software/sequencer.c
system_ddr3_0_s0_software/sequencer.h
system_ddr3_0_s0_software/core_debug_defines.h
system_ddr3_0_s0_software/sequencer_defines.h

I'm pretty certain the "..._sequencer_mem.hex" is the file that is loaded, but how do I regenerate this outside of using the qsys-generate command?

Ideally between steps 1) and 2) I want to change sequencer.c and rebuild the appropriate hex files in place...

I think the file: "system_ddr3_0_s0_make_qsys_seq.tcl" might be part of the solution, but this copies over the sequencer.c from the original location again....

Can someone provide any guidance or direction?

Many Thanks...

[edited for formatting]