Command help errors
Whilst reading through the command reference in the User Guide I've spotted a few errors in the help text.
1. The --set & --set-file options appear to be used in lots of commands where they're not used? e.g. alias, gui, etc.
2. gui: Text at top refers to '-t,--timeout=' option which doesn't exist.
3. lockclient: '-t,--timeout=' option should be --pyro-timeout?
4. get-global-config: typo - "will all settings".
5. broadcast: --raw option refers to '-s|--show' and --box refers to the 'show options'. Presumably meant to be --display & --display-task?

diff --git a/bin/cylc-broadcast b/bin/cylc-broadcast
index 24f39a9fd..13b0e9e29 100755
--- a/bin/cylc-broadcast
+++ b/bin/cylc-broadcast
@@ -163,11 +163,11 @@ parser.add_option( "-k", "--display-task", metavar="TASKID",
         "(NAME"+TaskID.DELIM+"TAG).", action="store", default=None, dest="showtask" )
 
 parser.add_option( "-b", "--box",
-        help="Use unicode box characters with the show options.",
+        help="Use unicode box characters with -d, -k.",
         action="store_true", default=False, dest="unicode" )
 
 parser.add_option( "-r", "--raw",
-        help="With -s|--show, print in raw Python format",
+        help="Write out the raw Python config structure, with -d and -k ",
         action="store_true", default=False, dest="raw" )
 
 ( options, args ) = parser.parse_args()
diff --git a/bin/cylc-diff b/bin/cylc-diff
index 17045110c..c7c04eb2a 100755
--- a/bin/cylc-diff
+++ b/bin/cylc-diff
@@ -108,7 +108,7 @@ default configuration values (e.g. the default job submission log
 directory.
 
 Files in the suite bin directory and other sub-directories of the 
-suite definition directory are not currently differenced.""", 
+suite definition directory are not currently differenced.""", jset=True,
     argdoc=[('REG1', 'Suite name'), ('REG1', 'Suite name')] )
 
 parser.add_option( "-n", "--nested", help="print suite.rc "
diff --git a/bin/cylc-get-config b/bin/cylc-get-config
index 23b866a90..7992cd4ce 100755
--- a/bin/cylc-get-config
+++ b/bin/cylc-get-config
@@ -57,7 +57,7 @@ $ cylc get-config --item=[runtime][modelX] foo.bar
 [[[environment]]]
     FOO = foo
     BAR = bar
-...""" )
+...""", jset=True )
 
 parser.add_option( "-i", "--item", metavar="[SEC...]ITEM", 
         help="The config item to print. Can be used multiple "
diff --git a/bin/cylc-get-global-config b/bin/cylc-get-global-config
index 0eb07c08a..afcf3e81a 100755
--- a/bin/cylc-get-global-config
+++ b/bin/cylc-get-global-config
@@ -22,7 +22,7 @@ from optparse import OptionParser
 parser = OptionParser( usage = """cylc [admin] get-global-config [OPTIONS] 
 
 Print settings determined by the cylc site and user configuration files,
-and auto-generate those files will all settings initially commented out.
+and generate example files with all settings initially commented out.
 
 1) $CYLC_DIR/conf/siterc/cfgspec  # legal items and default values
 2) $CYLC_DIR/conf/siterc/site.rc  # site file (overrides defaults)
diff --git a/bin/cylc-graph b/bin/cylc-graph
index ae381da90..89e21e89f 100755
--- a/bin/cylc-graph
+++ b/bin/cylc-graph
@@ -109,7 +109,7 @@ GRAPH VIEWER CONTROLS:
     * "group" - close this node's parent family.
     * "ungroup" - open this family node.
     * "recursive ungroup" - ungroup all families below this node.""",
-    argdoc = [('[REG]', 'Suite name'), 
+    jset=True, argdoc = [('[REG]', 'Suite name'), 
         ('[START]', 'Initial cycle time to plot (default=2999010100)'),
         ('[STOP]', 'Final cycle time to plot (default=2999010123)') ])
 
diff --git a/bin/cylc-gui b/bin/cylc-gui
index 31ac1d531..e7adc7367 100755
--- a/bin/cylc-gui
+++ b/bin/cylc-gui
@@ -38,14 +38,10 @@ Local suites can be opened and switched between from within gcylc. To
 connect to running remote suites (whose passphrase you have installed)
 you must currently use --host and/or --owner on the gcylc command line.
 
-If the '-t,--timeout=' option is used the timeout value will be passed
-on to the suite if it is subsequently started from the GUI (and it will
-in turn be passed to tasks submitted by the suite).
-
 Available task state color themes are shown under the View menu. To
 customize themes copy $CYLC_DIR/conf/gcylcrc/gcylc.rc.eg to
 $HOME/.cylc/gcylc.rc and follow the instructions in the file.""",
-pyro=True, noforce=True, gcylc=True, argdoc=[('[REG]', 'Suite name' )])
+pyro=True, noforce=True, jset=True, argdoc=[('[REG]', 'Suite name' )])
 
 ( options, args ) = parser.parse_args()
 
diff --git a/bin/cylc-list b/bin/cylc-list
index 6513729a2..a18bee8c8 100755
--- a/bin/cylc-list
+++ b/bin/cylc-list
@@ -37,7 +37,7 @@ for each namespace:
 The first-parent inheritance graph determines the primary task family
 groupings that are collapsible in gcylc suite views and the graph
 viewer tool. To visualize the full multiple inheritance hierarchy use:
-  'cylc graph -n'.""" )
+  'cylc graph -n'.""", jset=True )
 
 parser.add_option( "-a","--all-tasks",
         help="Print all tasks, not just those used in the graph.",
diff --git a/bin/cylc-lockclient b/bin/cylc-lockclient
index 72ac4782d..403177e27 100755
--- a/bin/cylc-lockclient
+++ b/bin/cylc-lockclient
@@ -115,8 +115,9 @@ See also:
             help="Print lockserver PID, log, and state filenames.",
             action="store_true", dest="get_filenames" )
 
-    parser.add_option( "-t", "--timeout", metavar='SECONDS',
-            help="Set a network connection timeout for Pyro.",
+    parser.add_option( "--pyro-timeout", metavar='SEC',
+            help="Set a timeout for Pyro network connections. The "
+            "default is no timeout.",
             action="store",default=None, dest="pyro_timeout" )
 
     #parser.add_option( "--debug",
diff --git a/bin/cylc-restart b/bin/cylc-restart
index e684de726..519ea0c76 100755
--- a/bin/cylc-restart
+++ b/bin/cylc-restart
@@ -59,8 +59,7 @@ suite from the local host requires the suite passphrase to be installed.
 Both /etc/profile and $HOME/.profile, if they exist, will be sourced on
 the remote host before starting the suite."""
 
-        self.parser = cop( usage,
-   argdoc=[("REG", "Suite name"),
+        self.parser = cop( usage, jset=True, argdoc=[("REG", "Suite name"),
    ( "[FILE]", """Optional state dump file, assumed to reside in the
                         suite state dump directory unless an absolute path
                         is given. Defaults to the most recent suite state.""")]) 
diff --git a/bin/cylc-run b/bin/cylc-run
index 2d4927d42..8d47d38ba 100755
--- a/bin/cylc-run
+++ b/bin/cylc-run
@@ -68,8 +68,7 @@ suite from the local host requires the suite passphrase to be installed.
 Both /etc/profile and $HOME/.profile, if they exist, will be sourced on
 the remote host before starting the suite.""" 
 
-        self.parser = cop( usage,
-                argdoc=[ ("REG", "Suite name"), 
+        self.parser = cop( usage, jset=True, argdoc=[ ("REG", "Suite name"), 
                 ("[START]", """Initial cycle time, optional if defined in the 
                         suite.rc file (in which case the command line
                         takes priority and a suite.rc final cycle time
diff --git a/bin/cylc-submit b/bin/cylc-submit
index 77f16a290..ce13bfb38 100755
--- a/bin/cylc-submit
+++ b/bin/cylc-submit
@@ -56,7 +56,7 @@ same registration, and only if the task is not locked (i.e. only if
 the same task, NAME.TAG, is not currently running in the suite)."""
 
 def commandline_parser():
-    parser = cop( usage, 
+    parser = cop( usage, jset=True,
             argdoc=[ ("REG", "Suite name"),
                 ("TASK", "Target task (NAME"+TaskID.DELIM+"TAG)")])
 
diff --git a/bin/cylc-suite-state b/bin/cylc-suite-state
index 1af9759af..803ead65c 100755
--- a/bin/cylc-suite-state
+++ b/bin/cylc-suite-state
@@ -79,9 +79,7 @@ Returns 0 if TASK at CYCLE has reached STATUS, 1 otherwise.
 
 The command can be run in polling mode with the --wait option.""")
 
-parser.remove_option("-s")
 parser.remove_option("--db")
-parser.remove_option("--set-file")
 parser.remove_option("--debug")
 
 parser.add_option( "-t", "--task", 
diff --git a/bin/cylc-validate b/bin/cylc-validate
index c8d31aa0a..445c21310 100755
--- a/bin/cylc-validate
+++ b/bin/cylc-validate
@@ -35,7 +35,7 @@ files held in $CYLC_DIR/conf/suiterc/.
 
 If the suite definition uses include-files reported line numbers
 will correspond to the inlined version seen by the parser; use 
-'cylc view -i,--inline SUITE' for comparison.""" )
+'cylc view -i,--inline SUITE' for comparison.""", jset=True )
 
 parser.add_option( "--strict", 
         help="Fail any use of unsafe or experimental features. "
diff --git a/bin/cylc-view b/bin/cylc-view
index 3e80b405c..24c76e3ce 100755
--- a/bin/cylc-view
+++ b/bin/cylc-view
@@ -50,7 +50,7 @@ Where <editor> is defined in the cylc site and user config files
 For remote host or owner, the suite will be printed to stdout unless
 the '-g,--gui' flag is used to spawn a remote GUI edit session.
 
-See also 'cylc [prep] edit'.""")
+See also 'cylc [prep] edit'.""", jset=True )
 
 parser.add_option( "--inline", "-i", 
         help="Inline any include-files.",
diff --git a/bin/reload.sh b/bin/reload.sh
deleted file mode 100755
index 1dbf52bf3..000000000
--- a/bin/reload.sh
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/bin/bash
-
-#C: THIS FILE IS PART OF THE CYLC SUITE ENGINE.
-#C: Copyright (C) 2008-2013 Hilary Oliver, NIWA
-#C: 
-#C: This program is free software: you can redistribute it and/or modify
-#C: it under the terms of the GNU General Public License as published by
-#C: the Free Software Foundation, either version 3 of the License, or
-#C: (at your option) any later version.
-#C:
-#C: This program is distributed in the hope that it will be useful,
-#C: but WITHOUT ANY WARRANTY; without even the implied warranty of
-#C: MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#C: GNU General Public License for more details.
-#C:
-#C: You should have received a copy of the GNU General Public License
-#C: along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-set -e
-
-# Shutdown, wait, restart. Use to reload suite changes without having to 
-# wait around for currently running tasks to finish prior to a manual
-# restart. Be aware that suite stdout and stderr will be reattached to
-# this process on the restart.
-
-# AWAITING INCORPORATION INTO THE MAIN CYLC INTERFACE, IF USEFUL.
-
-# NOTE: NOW WE CAN ACTUALLY RELOAD THE SUITE DEFINITION AT RUN TIME.
-
-SUITE=$1
-CYLC=$(dirname $0)/cylc
-
-$CYLC shutdown -f $SUITE
-
-echo "Waiting for $SUITE to shut down"
-echo -n "."
-
-while $CYLC ping $SUITE; do
-    sleep 1
-    echo -n "."
-done
-echo
-
-echo "Restarting $SUITE"
-$CYLC restart $SUITE
diff --git a/lib/cylc/CylcOptionParsers.py b/lib/cylc/CylcOptionParsers.py
index 418c0d786..b6b9c67d7 100644
--- a/lib/cylc/CylcOptionParsers.py
+++ b/lib/cylc/CylcOptionParsers.py
@@ -50,7 +50,7 @@ class db_optparse( object ):
 
 class cop( OptionParser ):
 
-    def __init__( self, usage, argdoc=[('REG', 'Suite name')], pyro=False, gcylc=False, noforce=False ):
+    def __init__( self, usage, argdoc=[('REG', 'Suite name')], pyro=False, noforce=False, jset=False ):
 
         # commands that interact with a running suite ("controlcom=True")
         # normally get remote access via Pyro RPC; but optionally
@@ -67,7 +67,7 @@ Arguments:"""
         self.n_optional_args = 0
         self.unlimited_args = False
         self.pyro = pyro
-        self.gcylc = gcylc
+        self.jset = jset
         maxlen = 0
         for arg in argdoc:
             if len(arg[0]) > maxlen:
@@ -143,20 +143,19 @@ Arguments:"""
                         "prompts have been disabled in the site/user config files.",
                         action="store_true", default=False, dest="force" )
 
-        if gcylc or not pyro:
+        if self.jset:
             self.add_option( "-s", "--set", metavar="NAME=VALUE",
-                help="Set the value of a template variable in the suite "
-                "definition; can be used multiple times to set multiple "
-                "variables.  WARNING: these settings do not persist "
-                "across restarts, you have to set them again on the "
-                "\"cylc restart\" command line.",
+                help="Set the value of a Jinja2 template variable in the suite "
+                "definition. This option can be used multiple times on the command "
+                "line.  WARNING: these settings do not persist across suite restarts; "
+                "they need to be set again on the \"cylc restart\" command line.",
                 action="append", default=[], dest="templatevars" )
 
             self.add_option( "--set-file", metavar="FILE",
-                help="Set the value of template variables in the suite "
+                help="Set the value of Jinja2 template variables in the suite "
                 "definition from a file containing NAME=VALUE pairs (one per line). "
-                "WARNING: these settings do not persist across restarts, you "
-                "have to set them again on the \"cylc restart\" command line.",
+                "WARNING: these settings do not persist across suite restarts; "
+                "they need to be set again on the \"cylc restart\" command line.",
                 action="store", default=None, dest="templatevars_file" )
 
     def parse_args( self ):
@@ -173,7 +172,7 @@ Arguments:"""
         options.db = foo.get_db_location()
         options.db_owner = foo.get_db_owner()
 
-        if self.gcylc or not self.pyro:
+        if self.jset:
             if options.templatevars_file:
                 options.templatevars_file = os.path.abspath( options.templatevars_file )
 
diff --git a/lib/cylc/gui/SuiteControl.py b/lib/cylc/gui/SuiteControl.py
index a050f031d..4f53cce02 100644
--- a/lib/cylc/gui/SuiteControl.py
+++ b/lib/cylc/gui/SuiteControl.py
@@ -881,7 +881,7 @@ been defined for this suite""").inform()
             optgroups, mode_live_rb, mode_sim_rb, mode_dum_rb, hold_cb,
             holdtime_entry ):
 
-        command = 'cylc control run --from-gui ' + self.cfg.template_vars_opts
+        command = 'cylc control run ' + self.cfg.template_vars_opts
         options = ''
         method = ''
         if coldstart_rb.get_active():
@@ -894,7 +894,7 @@ been defined for this suite""").inform()
             options += ' -r'
         elif restart_rb.get_active():
             method = 'restart'
-            command = 'cylc control restart --from-gui ' + self.cfg.template_vars_opts
+            command = 'cylc control restart ' + self.cfg.template_vars_opts
 
         if mode_live_rb.get_active():
             pass
@@ -903,9 +903,6 @@ been defined for this suite""").inform()
         elif mode_dum_rb.get_active():
             command += ' --mode=dummy'
 
-        if self.cfg.pyro_timeout:
-            command += ' --timeout=' + str(self.cfg.pyro_timeout)
-
         ctime = ''
         if method != 'restart':
             # start time
diff --git a/lib/cylc/scheduler.py b/lib/cylc/scheduler.py
index 59c17000f..39639baa2 100644
--- a/lib/cylc/scheduler.py
+++ b/lib/cylc/scheduler.py
@@ -149,9 +149,6 @@ class scheduler(object):
                 help="Do a test run against a previously generated reference log.",
                 action="store_true", default=False, dest="reftest" )
 
-        self.parser.add_option( "--from-gui", help= "(do not use).",
-                action="store_true", default=False, dest="from_gui" )
-
         self.parse_commandline()
 
         gcfg.print_deprecation_warnings()
@@ -269,7 +266,7 @@ class scheduler(object):
         self.initial_oldest_ctime = self.get_oldest_c_time()
 
         # REMOTELY ACCESSIBLE SUITE STATE SUMMARY
-        self.suite_state = state_summary( self.config, self.run_mode, self.initial_oldest_ctime, self.from_gui )
+        self.suite_state = state_summary( self.config, self.run_mode, self.initial_oldest_ctime )
         self.pyro.connect( self.suite_state, 'state_summary')
 
         # initial cycle time
@@ -797,11 +794,6 @@ class scheduler(object):
         else:
             self.logging_level = logging.INFO
 
-        if self.options.from_gui:
-            self.from_gui = True
-        else:
-            self.from_gui = False
-
     def configure_pyro( self ):
         # CONFIGURE SUITE PYRO SERVER
         self.pyro = pyro_server( self.suite, self.suite_dir, 
diff --git a/lib/cylc/state_summary.py b/lib/cylc/state_summary.py
index 39781d63b..996f36535 100644
--- a/lib/cylc/state_summary.py
+++ b/lib/cylc/state_summary.py
@@ -24,9 +24,8 @@ from TaskID import TaskID
 class state_summary( Pyro.core.ObjBase ):
     """supply suite state summary information to remote cylc clients."""
 
-    def __init__( self, config, run_mode, start_time, from_gui=False ):
+    def __init__( self, config, run_mode, start_time ):
         Pyro.core.ObjBase.__init__(self)
-        self.from_gui = from_gui
         self.task_summary = {}
         self.global_summary = {}
         # external monitors should access config via methods in this
@@ -93,7 +92,6 @@ class state_summary( Pyro.core.ObjBase ):
         global_summary[ 'stopping' ] = stopping
         global_summary[ 'will_pause_at' ] = will_pause_at
         global_summary[ 'will_stop_at' ] = will_stop_at
-        global_summary[ 'started from gui' ] = self.from_gui
         global_summary[ 'runahead limit' ] = runahead
         global_summary[ 'states' ] = all_states
 
['bin/cylc-broadcast', 'bin/cylc-view', 'bin/cylc-diff', 'lib/cylc/scheduler.py', 'bin/cylc-list', 'bin/cylc-gui', 'bin/cylc-graph', 'bin/cylc-lockclient', 'bin/cylc-get-global-config', 'bin/cylc-validate', 'bin/cylc-get-config', 'lib/cylc/CylcOptionParsers.py', 'bin/cylc-run', 'bin/cylc-suite-state', 'lib/cylc/state_summary.py', 'bin/cylc-submit', 'lib/cylc/gui/SuiteControl.py', 'bin/cylc-restart']