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update documentation and release notes
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README.md

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Current Release
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---------------
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ScaffCC is currently in an *alpha* release. Specifically, the release details are:
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- Version 3.1
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- Version 3.0
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- Release Date: August, 2017
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- Release Note: The current version is still an alpha release. Multiple new features are in active developement. For instance, .qasmf formart conforming to standardized QASM and optimization to parallel scheduler are expected to be included in the near term.
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- Release Date: February, 2018
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Supported Operating Systems
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---------------------------
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-r Generate resource estimate (default)
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-q Generate QASM
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-f Generate flattened QASM
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-b Generate OpenQASM
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-R Disable rotation decomposition
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-T Disable Toffoli decomposition
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-l Levels of recursion to run (default=1)

changelog.txt

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2018-02-06:
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Release version -v4.0
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Migrated to LLVM v6.0.
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Release version -v3.1
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Added ability to output OpenQASM (via -b flag for scaffold.sh).
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Released Braidflash v2.0, with improved simulation of magic state distillation overheads,
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including different distillation protocols and different factory layouts.
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Fixed bug in braidflash generating machine-dependent results due to uninitialized variable.

docs/Documentation.pdf

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docs/Documentation.tex

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\author{Ali JavadiAbhari, Adam Holmes, Shruti Patil, Jeff Heckey, Daniel Kudrow,\\ Pranav Gokhale, David Noursi, Lee Ehudin, \\
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Yongshan Ding, Xin-Chuan Ryan Wu, Yunong Shi}
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\date{August 2017}
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\date{February 2018}
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docs/ch-apps/chapter-apps.aux

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docs/ch-release/chapter-release.tex

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\section{Current Release}
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The current release of ScaffCC is:
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\begin{itemize}
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\item Version 3.0
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\item Alpha
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\item Release Date: August 6, 2017
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\item Version 3.1
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\item Release Date: February 4, 2018
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\end{itemize}
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\section{Supported Operating Systems}
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ScaffCC currently offers support for the following operating systems:

docs/ch-usage/chapter-usage.aux

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docs/ch-usage/chapter-usage.tex

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-r Generate resource estimate (default)
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-q Generate QASM
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-f Generate flattened QASM
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-b Generate OpenQASM
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-R Disable rotation decomposition
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-T Disable Toffoli decomposition
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-l Levels of recursion to run (default=1)

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