diff --git a/wlauto/commands/run.py b/wlauto/commands/run.py
index 12038b1e..57a78819 100644
--- a/wlauto/commands/run.py
+++ b/wlauto/commands/run.py
@@ -90,6 +90,7 @@ class RunCommand(Command):
         parser = AgendaParser()
         if os.path.isfile(args.agenda):
             parser.load_from_path(config, args.agenda)
+            shutil.copy(args.agenda, output.raw_config_dir)
         else:
             try:
                 pluginloader.get_plugin_class(args.agenda, kind='workload')
diff --git a/wlauto/core/configuration/configuration.py b/wlauto/core/configuration/configuration.py
index 0fb6b5cf..9b043a0d 100644
--- a/wlauto/core/configuration/configuration.py
+++ b/wlauto/core/configuration/configuration.py
@@ -541,10 +541,9 @@ class Configuration(object):
 
     def to_pod(self):
         pod = {}
-        for cfg_point in self.configuration.itervalues():
+        for cfg_point in self.config_points:
             value = getattr(self, cfg_point.name, None)
-            if value is not None:
-                pod[cfg_point.name] = _to_pod(cfg_point, value)
+            pod[cfg_point.name] = _to_pod(cfg_point, value)
         return pod
 
 
@@ -848,6 +847,16 @@ class JobSpec(Configuration):
         instance['id'] = job_id
         return instance
 
+    @property
+    def section_id(self):
+        if self.id is not None:
+            self.id.rsplit('-', 1)[0]
+
+    @property
+    def workload_id(self):
+        if self.id is not None:
+            self.id.rsplit('-', 1)[-1]
+
     def __init__(self):
         super(JobSpec, self).__init__()
         self.to_merge = defaultdict(OrderedDict)
@@ -1001,7 +1010,6 @@ class JobGenerator(object):
         return specs
 
 
-
 def create_job_spec(workload_entry, sections, target_manager, plugin_cache,
                     disabled_instruments):
     job_spec = JobSpec()
diff --git a/wlauto/core/configuration/manager.py b/wlauto/core/configuration/manager.py
index ef41be9f..b8bacd38 100644
--- a/wlauto/core/configuration/manager.py
+++ b/wlauto/core/configuration/manager.py
@@ -1,3 +1,7 @@
+import random
+from itertools import izip_longest, groupby, chain
+
+from wlauto.core import pluginloader
 from wlauto.core.configuration.configuration import (MetaConfiguration,
                                                      RunConfiguration,
                                                      JobGenerator, settings)
@@ -10,7 +14,7 @@ class CombinedConfig(object):
     @staticmethod
     def from_pod(pod):
         instance = CombinedConfig()
-        instance.settings = MetaConfiguration.from_pod(pod.get('setttings', {}))
+        instance.settings = MetaConfiguration.from_pod(pod.get('settings', {}))
         instance.run_config = RunConfiguration.from_pod(pod.get('run_config', {}))
         return instance
 
@@ -23,6 +27,24 @@ class CombinedConfig(object):
                 'run_config': self.run_config.to_pod()}
 
 
+class Job(object):
+
+    def __init__(self, spec, iteration, context):
+        self.spec = spec
+        self.iteration = iteration
+        self.context = context
+        self.status = 'new'
+        self.workload = None
+        self.output = None
+
+    def load(self, target, loader=pluginloader):
+        self.workload = loader.get_workload(self.spec.workload_name,
+                                            target,
+                                            **self.spec.workload_parameters)
+        self.workload.init_resources(self.context)
+        self.workload.validate()
+
+
 class ConfigManager(object):
     """
     Represents run-time state of WA. Mostly used as a container for loaded 
@@ -32,6 +54,26 @@ class ConfigManager(object):
     instance of wA itself.
     """
 
+    @property
+    def enabled_instruments(self):
+        return self.jobs_config.enabled_instruments
+
+    @property
+    def job_specs(self):
+        if not self._jobs_generated:
+            msg = 'Attempting to access job specs before '\
+                  'jobs have been generated'
+            raise RuntimeError(msg)
+        return [j.spec for j in self._jobs]
+
+    @property
+    def jobs(self):
+        if not self._jobs_generated:
+            msg = 'Attempting to access jobs before '\
+                  'they have been generated'
+            raise RuntimeError(msg)
+        return self._jobs
+
     def __init__(self, settings=settings):
         self.settings = settings
         self.run_config = RunConfiguration()
@@ -39,8 +81,9 @@ class ConfigManager(object):
         self.jobs_config = JobGenerator(self.plugin_cache)
         self.loaded_config_sources = []
         self._config_parser = ConfigParser()
-        self._job_specs = []
-        self.jobs = []
+        self._jobs = []
+        self._jobs_generated = False
+        self.agenda = None
 
     def load_config_file(self, filepath):
         self._config_parser.load_from_path(self, filepath)
@@ -50,7 +93,121 @@ class ConfigManager(object):
         self._config_parser.load(self, values, source)
         self.loaded_config_sources.append(source)
 
+    def get_plugin(self, name=None, kind=None, *args, **kwargs):
+        return self.plugin_cache.get_plugin(name, kind, *args, **kwargs)
+
+    def get_instruments(self, target):
+        instruments = []
+        for name in self.enabled_instruments:
+            instruments.append(self.get_plugin(name, kind='instrument', 
+                                               target=target))
+        return instruments
+
     def finalize(self):
+        if not self.agenda:
+            msg = 'Attempting to finalize config before agenda has been set'
+            raise RuntimeError(msg)
         self.run_config.merge_device_config(self.plugin_cache)
         return CombinedConfig(self.settings, self.run_config)
 
+    def generate_jobs(self, context):
+        job_specs = self.jobs_config.generate_job_specs(context.tm)
+        exec_order = self.run_config.execution_order
+        for spec, i in permute_iterations(job_specs, exec_order):
+            job = Job(spec, i, context)
+            job.load(context.tm.target)
+            self._jobs.append(job)
+        self._jobs_generated = True
+
+
+def permute_by_job(specs):
+    """
+    This is that "classic" implementation that executes all iterations of a
+    workload spec before proceeding onto the next spec.
+
+    """
+    for spec in specs:
+        for i in range(1, spec.iterations + 1):
+            yield (spec, i)
+ 
+
+def permute_by_iteration(specs):
+    """
+    Runs the first iteration for all benchmarks first, before proceeding to the
+    next iteration, i.e. A1, B1, C1, A2, B2, C2...  instead of  A1, A1, B1, B2,
+    C1, C2...
+
+    If multiple sections where specified in the agenda, this will run all
+    sections for the first global spec first, followed by all sections for the
+    second spec, etc.
+
+    e.g. given sections X and Y, and global specs A and B, with 2 iterations,
+    this will run
+
+    X.A1, Y.A1, X.B1, Y.B1, X.A2, Y.A2, X.B2, Y.B2
+
+    """
+    groups = [list(g) for k, g in groupby(specs, lambda s: s.workload_id)]
+
+    all_tuples = []
+    for spec in chain(*groups):
+        all_tuples.append([(spec, i + 1) 
+                           for i in xrange(spec.iterations)])
+    for t in chain(*map(list, izip_longest(*all_tuples))):
+        if t is not None:
+            yield t
+
+
+def permute_by_section(specs):
+    """
+    Runs the first iteration for all benchmarks first, before proceeding to the
+    next iteration, i.e. A1, B1, C1, A2, B2, C2...  instead of  A1, A1, B1, B2,
+    C1, C2...
+
+    If multiple sections where specified in the agenda, this will run all specs
+    for the first section followed by all specs for the seciod section, etc.
+
+    e.g. given sections X and Y, and global specs A and B, with 2 iterations,
+    this will run
+
+    X.A1, X.B1, Y.A1, Y.B1, X.A2, X.B2, Y.A2, Y.B2
+
+    """
+    groups = [list(g) for k, g in groupby(specs, lambda s: s.section_id)]
+
+    all_tuples = []
+    for spec in chain(*groups):
+        all_tuples.append([(spec, i + 1) 
+                           for i in xrange(spec.iterations)])
+    for t in chain(*map(list, izip_longest(*all_tuples))):
+        if t is not None:
+            yield t
+ 
+
+def permute_randomly(specs):
+    """
+    This will generate a random permutation of specs/iteration tuples.
+
+    """
+    result = []
+    for spec in specs:
+        for i in xrange(1, spec.iterations + 1):
+            result.append((spec, i))
+    random.shuffle(result)
+    for t in result:
+        yield t
+
+
+permute_map = {
+    'by_iteration': permute_by_iteration,
+    'by_job': permute_by_job,
+    'by_section': permute_by_section,
+    'random': permute_randomly,
+}
+
+
+def permute_iterations(specs, exec_order):
+    if exec_order not in permute_map:
+        msg = 'Unknown execution order "{}"; must be in: {}'
+        raise ValueError(msg.format(exec_order, permute_map.keys()))
+    return permute_map[exec_order](specs)
diff --git a/wlauto/core/configuration/parsers.py b/wlauto/core/configuration/parsers.py
index 37624a18..df6d019e 100644
--- a/wlauto/core/configuration/parsers.py
+++ b/wlauto/core/configuration/parsers.py
@@ -95,6 +95,8 @@ class AgendaParser(object):
             self._process_global_workloads(state, global_workloads, wkl_ids)
             self._process_sections(state, sections, sect_ids, wkl_ids)
 
+            state.agenda = source
+
         except (ConfigError, SerializerSyntaxError) as e:
             raise ConfigError('Error in "{}":\n\t{}'.format(source, str(e)))
 
@@ -156,7 +158,7 @@ class AgendaParser(object):
                                                    state.jobs_config)
                 workloads.append(workload)
 
-            section = _construct_valid_entry(section, seen_section_ids, 
+            section = _construct_valid_entry(section, seen_sect_ids, 
                                              "s", state.jobs_config)
             state.jobs_config.add_section(section, workloads)
 
diff --git a/wlauto/core/configuration/plugin_cache.py b/wlauto/core/configuration/plugin_cache.py
index e0d79a41..4c02192d 100644
--- a/wlauto/core/configuration/plugin_cache.py
+++ b/wlauto/core/configuration/plugin_cache.py
@@ -123,6 +123,11 @@ class PluginCache(object):
 
         return config
 
+    def get_plugin(self, name, kind=None, *args, **kwargs):
+        config = self.get_plugin_config(name)
+        kwargs = dict(config.items() + kwargs.items())
+        return self.loader.get_plugin(name, kind=kind, *args, **kwargs)
+
     @memoized
     def get_plugin_parameters(self, name):
         params = self.loader.get_plugin_class(name).parameters
diff --git a/wlauto/core/execution.py b/wlauto/core/execution.py
index 95d67602..3ac3a2dd 100644
--- a/wlauto/core/execution.py
+++ b/wlauto/core/execution.py
@@ -73,6 +73,19 @@ REBOOT_DELAY = 3
 
 
 class ExecutionContext(object):
+
+
+    def __init__(self, cm, tm, output):
+        self.logger = logging.getLogger('ExecContext')
+        self.cm = cm
+        self.tm = tm
+        self.output = output
+        self.logger.debug('Loading resource discoverers')
+        self.resolver = ResourceResolver(cm)
+        self.resolver.load()
+
+
+class OldExecutionContext(object):
     """
     Provides a context for instrumentation. Keeps track of things like
     current workload and iteration.
@@ -214,8 +227,8 @@ def _check_artifact_path(path, rootpath):
     return full_path
 
 
-
 class FakeTargetManager(object):
+    # TODO: this is a FAKE
 
     def __init__(self, name, config):
         self.device_name = name
@@ -286,9 +299,17 @@ class Executor(object):
         target_manager = init_target_manager(config.run_config)
         output.write_target_info(target_manager.get_target_info())
 
-        self.logger.info('Generationg jobs')
-        job_specs = config_manager.jobs_config.generate_job_specs(target_manager)
-        output.write_job_specs(job_specs)
+        self.logger.info('Initializing execution conetext')
+        context = ExecutionContext(config_manager, target_manager, output)
+
+        self.logger.info('Generating jobs')
+        config_manager.generate_jobs(context)
+        output.write_job_specs(config_manager.job_specs)
+
+        self.logger.info('Installing instrumentation')
+        for instrument in config_manager.get_instruments(target_manager.target):
+            instrumentation.install(instrument)
+        instrumentation.validate()
 
     def old_exec(self, agenda, selectors={}):
         self.config.set_agenda(agenda, selectors)
@@ -396,6 +417,12 @@ class Executor(object):
         signal.disconnect(self._warning_signalled_callback, signal.WARNING_LOGGED)
 
 
+class Runner(object):
+    """
+    
+    """
+
+
 class RunnerJob(object):
     """
     Represents a single execution of a ``RunnerJobDescription``. There will be one created for each iteration
@@ -410,7 +437,7 @@ class RunnerJob(object):
         self.result = IterationResult(self.spec)
 
 
-class Runner(object):
+class OldRunner(object):
     """
     This class is responsible for actually performing a workload automation
     run. The main responsibility of this class is to emit appropriate signals
diff --git a/wlauto/core/instrumentation.py b/wlauto/core/instrumentation.py
index db2db8ce..6bba95c5 100644
--- a/wlauto/core/instrumentation.py
+++ b/wlauto/core/instrumentation.py
@@ -380,9 +380,9 @@ class Instrument(Plugin):
     """
     kind = "instrument"
 
-    def __init__(self, device, **kwargs):
+    def __init__(self, target, **kwargs):
         super(Instrument, self).__init__(**kwargs)
-        self.device = device
+        self.target = target
         self.is_enabled = True
         self.is_broken = False
 
diff --git a/wlauto/core/output.py b/wlauto/core/output.py
index 1047bf2f..77d5853e 100644
--- a/wlauto/core/output.py
+++ b/wlauto/core/output.py
@@ -93,6 +93,10 @@ class RunOutput(object):
     def jobsfile(self):
         return os.path.join(self.metadir, 'jobs.json')
 
+    @property
+    def raw_config_dir(self):
+        return os.path.join(self.metadir, 'raw_config')
+
     def __init__(self, path):
         self.basepath = path
         self.info = None
diff --git a/wlauto/core/plugin.py b/wlauto/core/plugin.py
index f614169b..ccf2dece 100644
--- a/wlauto/core/plugin.py
+++ b/wlauto/core/plugin.py
@@ -557,6 +557,8 @@ class PluginLoader(object):
     def update(self, packages=None, paths=None, ignore_paths=None):
         """ Load plugins from the specified paths/packages
         without clearing or reloading existing plugin. """
+        msg = 'Updating from: packages={} paths={}'
+        self.logger.debug(msg.format(packages, paths))
         if packages:
             self.packages.extend(packages)
             self._discover_from_packages(packages)
@@ -572,6 +574,7 @@ class PluginLoader(object):
 
     def reload(self):
         """ Clear all discovered items and re-run the discovery. """
+        self.logger.debug('Reloading')
         self.clear()
         self._discover_from_packages(self.packages)
         self._discover_from_paths(self.paths, self.ignore_paths)
@@ -591,7 +594,8 @@ class PluginLoader(object):
             raise ValueError('Unknown plugin type: {}'.format(kind))
         store = self.kind_map[kind]
         if name not in store:
-            raise NotFoundError('plugins {} is not {} {}.'.format(name, get_article(kind), kind))
+            msg = 'plugins {} is not {} {}.'
+            raise NotFoundError(msg.format(name, get_article(kind), kind))
         return store[name]
 
     def get_plugin(self, name=None, kind=None, *args, **kwargs):
diff --git a/wlauto/core/resolver.py b/wlauto/core/resolver.py
index e68cec4f..ba643b0d 100644
--- a/wlauto/core/resolver.py
+++ b/wlauto/core/resolver.py
@@ -48,7 +48,7 @@ class ResourceResolver(object):
 
         """
 
-        for rescls in self.config.ext_loader.list_resource_getters():
+        for rescls in pluginloader.list_resource_getters():
             getter = self.config.get_plugin(name=rescls.name, kind="resource_getter", resolver=self)
             getter.register()
 
diff --git a/wlauto/instrumentation/misc/__init__.py b/wlauto/instrumentation/misc/__init__.py
index 86c880fd..a02793b0 100644
--- a/wlauto/instrumentation/misc/__init__.py
+++ b/wlauto/instrumentation/misc/__init__.py
@@ -207,8 +207,8 @@ class ExecutionTimeInstrument(Instrument):
 
     priority = 15
 
-    def __init__(self, device, **kwargs):
-        super(ExecutionTimeInstrument, self).__init__(device, **kwargs)
+    def __init__(self, target, **kwargs):
+        super(ExecutionTimeInstrument, self).__init__(target, **kwargs)
         self.start_time = None
         self.end_time = None
 
diff --git a/wlauto/utils/types.py b/wlauto/utils/types.py
index 8e4c5e65..7b13f979 100644
--- a/wlauto/utils/types.py
+++ b/wlauto/utils/types.py
@@ -404,6 +404,7 @@ class toggle_set(set):
     def to_pod(self):
         return list(self.values())
 
+
 class ID(str):
 
     def merge_with(self, other):