Moved all files under doc/manual subfolder.

doc/manual/.gitignore

doc/manual/LICENSE.md

doc/manual/Makefile

doc/manual/README.md

doc/manual/src/Makefile

doc/manual/src/source/_static/custom.css

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doc/manual/src/source/_static/mathjax

doc/manual/src/source/_templates/about.html

doc/manual/src/source/_templates/navigation.html

doc/manual/src/source/bibliography.rst

doc/manual/src/source/conf.py

doc/manual/src/source/dynare-misc-commands.rst

doc/manual/src/source/examples.rst

doc/manual/src/source/index.rst

doc/manual/src/source/installation-and-configuration.rst

doc/manual/src/source/introduction.rst

doc/manual/src/source/reporting.rst

doc/manual/src/source/running-dynare.rst

doc/manual/src/source/the-configuration-file.rst