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Compiling without the amalgamation process
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Okay, so right now I got to change the `main.mk` a bit and finally got it to work. 

So for future reference: 

* I have a first `make` pass where I don't change any file (to compile `lemon`, possibly among others)
* Then, I edit `Makefile.linux-gcc` and replace all occurrences of `gcc` with `gcc -x none`
* I change `main.mk` and add change the executable target by adding `-lstdc++` at the end:

```
sqlite3$(EXE):	shell.c libsqlite3.a sqlite3.h
	$(TCCX) $(READLINE_FLAGS) -o sqlite3$(EXE) $(SHELL_OPT) \
		shell.c libsqlite3.a $(LIBREADLINE) $(TLIBS) $(THREADLIB) -lstdc++
```

* I run make again using `make -f Makefile.linux-gcc` and get my `sqlite3` executable as expected.

Thanks everyone for your support, you were of great help.