Eliminate duplicate Python source files in doc/.src/chapters

- Update symlinks in doc/.src/book/src-* to point directly to src/
  instead of doc/.src/chapters/*/src-*
- Delete duplicate src-* directories from doc/.src/chapters/
  (advec, diffu, formulas, nonlin, softeng2, trunc, vib, wave)
- Move formulas source files to src/formulas/ (new directory)
- Fix @@@code directive in vib_app.do.txt for updated imports

This consolidates all Python source code in the src/ directory,
eliminating ~18k lines of duplicated code while preserving the
@@@code references via updated symlinks.

Author: ggorman

doc/.src/book/src-advec

@@ -1 +1 @@
-../chapters/advec/src-advec
+../../../src/advec

doc/.src/book/src-diffu

@@ -1 +1 @@
-../chapters/diffu/src-diffu
+../../../src/diffu

doc/.src/book/src-formulas

@@ -1 +1 @@
-../chapters/formulas/src-formulas
+../../../src/formulas

doc/.src/book/src-nonlin

@@ -1 +1 @@
-../chapters/nonlin/src-nonlin
+../../../src/nonlin

doc/.src/book/src-softeng2

@@ -1 +1 @@
-../chapters/softeng2/src-softeng2
+../../../src/softeng2

doc/.src/book/src-trunc

@@ -1 +1 @@
-../chapters/trunc/src-trunc
+../../../src/trunc

doc/.src/book/src-vib

@@ -1 +1 @@
-../chapters/vib/src-vib
+../../../src/vib

doc/.src/book/src-wave

@@ -1 +1 @@
-../chapters/wave/src-wave
+../../../src/wave