more dynamic stitching bug fixes

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13092 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
API: 'acqusition' -> 'acquisition'.

The misspelled methods are kept in MMStudioMainFrame for backward
compatibility, but have been removed from ScriptInterface.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13093 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
API: Deprecate ScriptInterface methods exposing internal classes.

There are still leaks through other API classes.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13094 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
More code cleanup trying to stay as much as possible behind the Micro-Manager api

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13095 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
added CustomAcqEngine.java

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13096 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Refactored into a new navigator plugin

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13097 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
added Util class

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13098 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
Remove several compiler warnings caused by depreciation of a number of functions

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13099 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13100 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
PI_GCS_2: Patch from Steffen with multiple updates:

- added support for C-865
- added support for E-816 (built into E-665, E-625, E-621) with
firmware older than 2.11 (this FW versions cannot be updated by
customer)
- added E-709 and C-884 as preconfigured controller
- changed default name of axis to "1" and "2"
- fixed problem with C-867.262 (initialization in endless loop, so
micro-manager is blocked by PI_GCS_2 adapter)
- added new keywords, so "Homing Mode" accepts "FRF", "FNL" and "FRF"
- added more helpful error codes and error messages
- improved code quality (using PCLint)

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13101 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
PI_GCS_2: Fix a VC++ warning.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13102 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
remove unthrown exception

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13103 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
GUI creation beginnings and many other updates

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13104 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
[nggb] Eliminate DEVICEADAPTERPATH.

Fix the infinite recursion of pkglibdir introduced in r13066-13067.
DEVICEADAPTERPATH did not play any useful role that could not be
replaced by simply setting pkglibdir, anyway.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13105 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13106 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
New OS X build: Add flag for incremental build.

To facilitate testing of the script.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13107 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
[nggb] Fix MMCorePy.py installation.

Need to use install-exec-hook, not install-exec-local, to ensure that the
destination directory has been created. Otherwise, /usr/bin/install (at least
on OS X) ends up copying MMCorePy.py to a _file_ named $pkglibdir.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13108 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
New OS X build: Use correct prefix.

The --prefix flag intended for building dependencies was leaking into the
configure command line for Micro-Manager itself.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13109 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
[nggb] Normalize installation for JARs and scripts.

All JARs now to to subdirectories of $(pkgdatadir). This temporarily
"breaks" the build, in the sense that mmstudio will not be able to find
the JARs in those locations. This should be fixed later so that a
typical Unix-style installation can work (with a correct launcher script
providing the search paths as Java system properties). However, for now,
these changes to the build system are sufficient to ensure that the
files go to a sensible, ImageJ-independent location; the packaging
script for the OS X binary package can deal with placing the files in
the correct final location for the portable app.

Also use semi-correct methods for clean.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13110 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
[nggb] Don't make installed MMCorePy.py executable.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@13111 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd