Fortran strategy to debug compilation errors - compilation

Question

I'm having a hard time debugging a compilation error in gfortran. My compiler is:
gfortran -v
Thread model: posix
gcc version 4.9.2 (x86_64-posix-seh-rev4, Built by MinGW-W64 project)
I can't include the real problem because it's too big. Below I'll discuss a model problem of what's happening:
I have one big module, let's call it ops, that I'd like to break down into several modules (e.g. add, subtract, multiply, divide, etc). To do this, I "use" modules "add" and "subtract" in module "ops", make the routines from "add" and "subtract" public, and then call the routines in "add" and "subtract" from the main program, which only uses "ops".
In this simple example (illustrated below in a simple program), using both modules works fine, and there are no errors. But when I do this with my big program, I get an error when trying to use the "subtract" module (I've also included what I mean in the program comments).
Here's the sample of the scenario:
module add_mod
private
public :: add
interface add; module procedure add1; end interface
contains
subroutine add1(a,b,c)
integer,intent(inout) :: a
integer,intent(in) :: b,c
a = b + c
end subroutine
end module
module subtract_mod
private
public :: subtract
interface subtract; module procedure subtract1; end interface
contains
subroutine subtract1(a,b,c)
integer,intent(inout) :: a
integer,intent(in) :: b,c
a = b - c
end subroutine
end module
module ops
use add_mod
! use subtract_mod ! Removing comment causes error...
private
public :: init
public :: add
! public :: subtract ! Removing comment causes error...
contains
subroutine init(a,b,c)
implicit none
integer,intent(inout) :: a,b,c
a = 0; b = 0; c = 0
end subroutine
end module
program test
use ops
implicit none
integer :: a,b,c
b = 1; c = 1
call add(a,b,c)
write(*,*) 'a,b,c = ',a,b,c
! call subtract(a,b,c) ! want to call...
write(*,*) 'a,b,c = ',a,b,c
end program
The error that I'm getting (in terms of the simplified example) is:
\add.o
\subtract.o
\subs.o
\main.o
gfortran: error: main.o: No such file or directory
make: *** [main] Error 1
The error from my big example looks like
C:\\Users\\charl\\Documents\\obj\parametricStudy.o
gfortran: error: C:\\Users\\charl\\Documnts\\obj\parametricStudy.o: No such file or directory
make: *** [C:\\Users\\charl\\Documents\\MOONS] Error 1
Where "parametricStudy" is the main program and "MOONS" is the name of the target/executable.
This really does not look like an error in terms of finding the executable, it looks like the executable is not made because of some other issue, but I don't have enough information to find out why. I've tried including all of the debugging flags I can think of:
fimplicit-none -Wuninitialized -cpp -fopenmp -Wall -Wextra -fbacktrace -fcheck=all -O0 -Og
Sorry for the long introduction, but here's my question: How can I debug this? I'm sorry if this was a poorly conveyed question, but I can't re-produce this error in a simple case, so I'm not sure how else to pose the question. Any help on a solution, debugging advice or improving this question is greatly appreciated!
UPDATE:
After seeing the comment about the compilation error typo, I tried reversing the order of the used modules. That is, now I tried using "subtract" alone, which works fine, but then try using "add" (together) and I get the same error. I'm now beginning to think that this is a compiler bug or something.
UPDATE 2:
I uploaded the code to github. It can be downloaded at
https://github.com/charliekawczynski/MOONS
The makefile is in the directory
\MOONS\makefiles\MOONS
And the output should show up in out_dir. To compile this, the $TARGET_DIR$ and $SRC_DIR$ must be defined. Please note that right now it is defined with the variable $USER$.
After changing the directory, I see a different misspelling (which seems to change when I make small changes in the code, e.g. removing some warnings related to unused variables).
UPDATE 3:
I've been removing more warnings related to un-used routines and variables, and now I see that the error still exists, but (as far as I see) there is no typo. Here is the new output:
gfortran -o
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\MOONS -J"
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\mod" -fimplicit-none -Wuninitialized -cpp -D_DOUBLE_PRECISION_ -D_FFT_RADIX2_ -fopenmp -Wall -Wextra -fbacktrace -fcheck=all -O0 -Og -D_DEBUG_DEL_ -D_DEBUG_INTERP_ -D_DEBUG_APPLYBCS_
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\IO_tools.o
...
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\init_Ufield.o
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\init_Pfield.o
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\energySolver.o
...
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\MOONS.o
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\richardsonExtrapolation.o
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\convergenceRate.o
C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\parametricStudy.o
gfortran: error: C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\obj\init_Pfield.: No such file or directory
make: *** [C:\\Users\\charl\\Documents\\GitHub\\MOONS\\out_dir\\MOONS] Error 1
C:\Users\charl\Documents\GitHub\MOONS\makefiles\MOONS>
I'm going to try a newer compiler and see if this fixes the problem