Small improvements to user manual
* Moved `COPYING.md`, `CODE_OF_CONDUCT.md`, `CONTRIBUTING.md`, and `LICENSE` (download only) into user manual #177. * Fixed formatting of GMSH command #177. * Fixed various links in existing documentation. * Updated link to user manual in CLI. * Added hints on cook book to `README.md` and user manual index. * Fix render of `README.md` tables in user manual.
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doc/markdown/CONTRIBUTING.md
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doc/markdown/COPYING.md
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doc/markdown/LICENSE
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