[vcpkg macos ci] Switch to using our own base boxes, to fix bringing up mac machines (#13619)

* [vcpkg ci:osx] Remove brew install

* add instructions for creating a new vagrant box

* fix the vagrant scripts for the new box

* finish fixing the setup

* [mecab jxrlib] fix ports for CI

mecab needed to use an actual ref that wasn't master,
and jxrlib needed a patch for xcode 12 CLTs.

Additionally, this fixes the mecab version to be a date, the date of the last commit,
since `1.0` is not the correct version (mecab doesn't have released versions)

* [many ports] fix compile with Xcode 12 CLTs

This mostly means fixing errors on implicit-function-declaration,
and removing some Werrors
* alac-decoder
* apr
* argtable2
* arrow
* hyperscan
* mcpp
* minizip
* mosquitto
* stormlib

* [many ports] even more Xcode 12 CLT fixes

* [jxrlib darknet] fix the last ports! (hopefully)

* CRs, plus minor wip changes to osx scripts

3 files changed, 44 insertions, 3 deletions

diff --git a/ports/cfitsio/0001-correct-headers-for-getcwd.patch b/ports/cfitsio/0001-correct-headers-for-getcwd.patch
new file mode 100644
index 000000000..afd63b61a
--- /dev/null
+++ b/ports/cfitsio/0001-correct-headers-for-getcwd.patch
@@ -0,0 +1,40 @@
+From 67400fcbd3ab2f7e68a8e7a60139b1b615debae2 Mon Sep 17 00:00:00 2001
+From: Nicole Mazzuca <mazzucan@outlook.com>
+Date: Wed, 23 Sep 2020 10:27:43 -0700
+Subject: [PATCH] correct headers for getcwd
+
+---
+ fitsio.h | 3 +++
+ group.c  | 2 +-
+ 2 files changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/fitsio.h b/fitsio.h
+index ec26d9d..792bb95 100644
+--- a/fitsio.h
++++ b/fitsio.h
+@@ -39,6 +39,9 @@ SERVICES PROVIDED HEREUNDER."
+ #define CFITSIO_MAJOR 3
+ #define CFITSIO_SONAME 5
+ 
++/* Required for getcwd() */
++#define _POSIX_C_SOURCE 200112L
++
+ /* the SONAME is incremented in a new release if the binary shared */
+ /* library (on linux and Mac systems) is not backward compatible */
+ /* with the previous release of CFITSIO */
+diff --git a/group.c b/group.c
+index 9326c57..cec0f6a 100644
+--- a/group.c
++++ b/group.c
+@@ -24,7 +24,7 @@
+ #include <direct.h>   /* defines the getcwd function on Windows PCs */
+ #endif
+ 
+-#if defined(unix) || defined(__unix__)  || defined(__unix) || defined(HAVE_UNISTD_H)
++#if defined(unix) || defined(__unix__)  || defined(__unix) || defined(__APPLE__) || defined(HAVE_UNISTD_H)
+ #include <unistd.h>  /* needed for getcwd prototype on unix machines */
+ #endif
+ 
+-- 
+2.24.3 (Apple Git-128)
+
diff --git a/ports/cfitsio/CONTROL b/ports/cfitsio/CONTROL
index c46eaadfe..e7a638303 100644
--- a/ports/cfitsio/CONTROL
+++ b/ports/cfitsio/CONTROL
@@ -1,4 +1,5 @@
 Source: cfitsio
-Version: 3.410-3
+Version: 3.410
+Port-Version: 4
 Homepage: https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
 Description: Library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format
diff --git a/ports/cfitsio/portfile.cmake b/ports/cfitsio/portfile.cmake
index c14b6743c..12e3e2d4a 100644
--- a/ports/cfitsio/portfile.cmake
+++ b/ports/cfitsio/portfile.cmake
@@ -1,5 +1,3 @@
-include(vcpkg_common_functions)
-
 vcpkg_download_distfile(ARCHIVE
     URLS "http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3410.tar.gz"
     FILENAME "cfitsio3410.tar.gz"
@@ -9,6 +7,8 @@ vcpkg_download_distfile(ARCHIVE
 vcpkg_extract_source_archive_ex(
     OUT_SOURCE_PATH SOURCE_PATH
     ARCHIVE ${ARCHIVE}
+    PATCHES
+        0001-correct-headers-for-getcwd.patch
 )
 
 vcpkg_configure_cmake(