updated from master

.gitignore

@@ -11,7 +11,6 @@ sysroots
 .pydevproject
 html
 *.directory
-*.kate-swp
 doxygen.tag
 # auto-generated files from x393 project
 src/drivers/elphel/x393.c
@@ -21,4 +20,4 @@ src/drivers/elphel/x393_map.h
 src/drivers/elphel/x393_types.h
 all_sources.lst
 excluding.lst
-attic
+attic
\ No newline at end of file

README.md

 # linux-elphel
-Extras (drivers, etc.) and patches for the kernel
+This project handles kernel drivers and driver modification for Elphel NC393 seriees cameras.
+The best way to install it is by running installation script in the top project -
+https://github.com/Elphel/elphel393 as different parts of the camera software are inter-dependent,
+and some of the required header files are generated from the Verilog code in
+[x393 FPGA project](https://github.com/Elphel/x393).
 
-##Downloading
-Code must be located in `poky/` directory. Navigate to `poky/` and run:
-```
-git clone https://github.com/Elphel/linux-elphel.git
-```
-##Generating links and headers
-Links between project tree and kernel source tree are generated by Bitbake during 'link' task when using `meta-elphel393`. Some required header files are automatically generated during the build process.
-```
-. ./oe-init-build-env
-bitbake linux-xlnx -c clean -f
-bitbake linux-xlnx -c link -f
-bitbake linux-xlnx -f
-```
-##Importing project into Eclipse
-Run Eclipse from its location directory and provide additional heap memory to it.
-```
-./eclipse -vmargs -Xmx4G
-```
-or just edit eclipse.ini (same directory as eclipse executable) and make sure -Xmx has at least 4G
+This is Eclipse CDT project, and the [setup sctipt](https://github.com/Elphel/elphel393) copies
+project configuration (.project, .cproject, .settings) from eclipse_project_setup subdirectory.
+Eclipse should be started after Linux kernel is built with `bitbake linux-xlnx` at least once
+so all the required files are already present. Then you may import *linux-elphel* as
+'existing Git project' in Eclipse (you need either Eclipse for C/C++ development or intall [CDT
+plugin](https://eclipse.org/cdt/) separately.
 
- - File → Import... → General → Existing Project into Workspace
- - [Next] → Select root directory → Browse → specify project location (`poky/linux-elphel/`) → [OK] → [Finish]
+Do not run `bitbake linux-xlnx -c clean` while the project is open in Eclipse - this command
+will delete all he staged files (kernel sources) and Eclipse will reset all file filters, so
+*.cproject* file will have to be restored from *eclipse_project_setup*. 
 
-Project now is imported into Eclipse workspace.
+Source files in Yocto project are staged (downloaded and optionally patched), so `-c clean` re-downloads
+files and erases any of your files or changes if they were made in the source directory tree.
+*linux-elphel* project keeps all the modified or new files in a sparse copy of the Linux kernel tree (*src*
+sub-directory) and the bitbake recipe (`bitbake linux-xlnx -c link`) adds symlinks to the actual
+project files. When the full kernel is opened in Eclipse, the base kernel files are from the staging
+area (so will be refreshed after `-c clean`) and the project files edits will stay safe in the *src*
+subdirectory.
+
+The khelper.py script is used to generate filters for the kernel by collecting information - which
+files where accessed during `bitbake linux-xlnx -c compile -f`, results are injected into *.cproject*
+configuratgion file, so any of the Linux kernel files that were not accessed during build will be marked
+as excluded from build (crossed out) and not resolved by the indexer.
 
- - Project → Properties
- - C/C++ General → Preprocessor Include Paths → Entries → GNU C → CDT User Settings
-   - [Add...] → Select "Preprocessor macros file" → `linux/include/generated/autoconf.h` → [OK]
-   - [Add...] → Select "Preprocessor macros file" → `linux/include/linux/compiler.h` → [OK]
-   - [Add...] → Select "Include file" → `linux/include/linux/kconfig.h` → [OK]
- - C/C++ General → Indexer
-   - Check “Enable project specific setttings”
-   - Check “Enable indexer”
-   - Uncheck “Index source files not included in the build”
-   - Uncheck “Index unused headers”
-   - Check “Index header variants”
-   - Uncheck “Index source and header files opened in editor”
-   - Uncheck “Allow heuristic resolution of includes”
-   - Set size of files to be skipped >100MB (effectively disabling this feature)
-   - Uncheck all “Skip…” options
- - [OK] to close the Advanced Settings window.
- - Project → C/C++ Index → Rebuild

khelper.py

@@ -2,21 +2,53 @@
 # encoding: utf-8
 from __future__ import division
 from __future__ import print_function
+"""
+# @file khelper.py
+# @brief Extract file access data after build, modify CDT project configuration
+# (.cproject) accordingly
+# @copyright Copyright (C) 2016, Elphel.inc.
+# @param <b>License</b>
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http:#www.gnu.org/licenses/>.
+
+@author:     Andrey Filippov
+@license:    GPLv3.0+
+@contact:    andrey@elphel.coml
+@deffield    updated: Updated
+"""
+__author__ = "Andrey Filippov"
+__copyright__ = "Copyright 2016, Elphel, Inc."
+__license__ = "GPL"
+__version__ = "3.0+"
+__maintainer__ = "Andrey Filippov"
+__email__ = "andrey@elphel.com"
+__status__ = "Development"
+
 import sys
 import os
 import time
 import xml.etree.ElementTree as ET
 '''
-TODO: make 2 runs, first before
-bitbake linux-xlnx
-khelper.py linux -1
-#get timestamp
-#next 2 commands - I do not understand why their access timestamp is set during previous command and does not change during bitbake 
-touch /home/eyesis/git/elphel393/linux-elphel/src/drivers/ata/ahci_elphel.c
-touch /home/eyesis/git/elphel393/linux-elphel/src/drivers/elphel/sensor_common.c
-bitbake linux-xlnx -c compile -f
-khelper.py linux <timestamp_from_the_first_run>
-             
+TODO:Automate, find out why separate touch commands are needed
+Run this program twice:
+1-st run ./khelper.py linux -1
+and save shown timestamp
+Then run (some mystery here)
+touch src/drivers/ata/ahci_elphel.c
+touch src/drivers/elphel/sensor_common.c
+Wait 5 seconds and run (in a different console with appropriate sourcing)
+bitbake linux-xlnx -c compile -f 
+Then again
+./khelper.py linux <timestamp_from_the_first_run>
+If somethong went wrong you will need to resore .cproject from eclipse_project_setup directory
 '''
 def file_tree(flist): # Each file in list is a file, no directories
     ftree={}