Added semantic checking for dangling bonds. 
New feature: Semantic errors now return a RuntimeException with a
BNGSemanticException object in the cause field
Merge branch 'master' of https://code.google.com/p/bionetgen
adding missing file. (exception)
added some auxiliary methods
auxiliary file
superficial changes to README_FIRST.txt and Network3/INSTALL
Modified CMakeLists.txt
Small change to CMakeLists.txt
argh
Renamed Makefile.old to Makefile.cmake and removed GSL dependencies
Added action addConcentration() to BNGModel.pm. Also created method SpeciesList->checkOrInitConcentrations() that is responsible for loading Model->Concentrations() before any method call that needs to work with concentreations. Finally, added a validation model: test_setconc.bngl
Merge branch 'master' of https://code.google.com/p/bionetgen
small change to rand2.cpp
Conflict resolution: BNGModel.pm
Fixed bug in Network3 that caused segfault on some systems.  Added quotes around RUN_NETWORK_VERSION argument.
Merge branch 'master' of https://code.google.com/p/bionetgen
Merge branch 'master' of https://code.google.com/p/bionetgen
(1) Removed default simulation configuration for PLA. User must now
define configuration using 'pla_config' argument in simulate_pla (or
simulate).
(2) Added a check for negative rates in SSA simulations. If a negative
rate is encountered an error message is thrown and the simulation is
terminated.
(3) Small change to catpath call in validate_examples.pl that was
causing an error message to be thrown during validation.
1) Changes to BNG2 signal handling: catches INT and TERM signals and relays to child process (rather than process group). 2) Simulate and Simulate_nf methods save child PID on a global variable so the signal handler knows where to find the child process. 3) Changed the way Open3 calls run_network and NFsim: command tokens are placed in the @command array without shell metacharacters (rather than string concatenation with metacharacters to separate token)s. This avoids the creation of an interediate shell that processes the metacharacters. Consequently, the PID returned by Open3 is the correct PID for run_network or NFsim. 4) Changes 1-3 were also applied to scan_var.pl
Fixed print_network() in network.cpp to print 'parameters' and
'functions' blocks and removed printing of 'reaction_rates' block. The
resulting .net file is now readable by run_network. Also modified PLA
code to support -n ('print_net') and -e ('print_end_net')
options.