taosolver_fg.c edited online with Bitbucket

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of //faq.html since the automatic tool incorrectly replaced /faq.html to //faq.html in some locations

These are largely updates of http to https but have a variety of other website location changes

Once this branch is in master individual developers can run make checkbadURLS and fix URLs related to their projects manually

Commit-type: bug-fix, documentation

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Deprecate old {Mat|PC|KSP}ComputeExplicitOperator in favor of {Mat|PC|KSP}ComputeOperator

{Mat|PC|KSP}ComputeExplicitOperator: add extra argument for matrix type

documentation and manual fixes for least-squares codes

ex4: set up shell for soft thresholding

tao ex4: TAOSHELL softthresh

tao ex4: separable fix. wip

tao ex4: implemented separable obj in ADMM

Tao ex4: cleanup

wip: s_norm convergence issue

wip

T

ex4: set up shell for soft thresholding

tao ex4: TAOSHELL softthresh

tao ex4: separable fix. wip

tao ex4: implemented separable obj in ADMM

Tao ex4: cleanup

wip: s_norm convergence issue

wip

Tao ex4: fix signs

Consistently follow the scaled dual variable formulation of ADMM

Tao ex4: update TaoShell syntax

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Tao: start TAOSHELL

For the user to give their own optimization implementation

TAOSHELL: add setsolve interface function

TAOSHELL: add missing file

Tao Shell: more direct copy of what's in SNES S

Tao: start TAOSHELL

For the user to give their own optimization implementation

TAOSHELL: add setsolve interface function

TAOSHELL: add missing file

Tao Shell: more direct copy of what's in SNES Shell

TaoShell: fix doc

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TAOSetUpdate: change the Update callback

In SNES, the update function does not uses contexts, and thus it does not appear in the callback prototype
With TAO, since we are explcitily passing the ctx

TAOSetUpdate: change the Update callback

In SNES, the update function does not uses contexts, and thus it does not appear in the callback prototype
With TAO, since we are explcitily passing the ctx via TAOSetUpdate, we have to give it back to the user when performing the call

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Merge remote-tracking branch 'origin/jczhang/vecscat-in-sf' [PR #1396]

Use new vector read-lock function names

The new one are VecLockReadPush, VecLockReadPop, VecSetErrorIfLocked

added D matrix for L1 norm