fix links

Author: knopers8

README.md

@@ -28,7 +28,7 @@ What is your use case?
 
     * My software is a command line utility with no state machine
 
-        :palm_tree: Nothing to do, AliECS natively supports generic commands. Make sure the task template for your command sets the control mode to `basic` ([see example](https://github.com/AliceO2Group/ControlWorkflows/blob/basic-tasks/tasks/sleep.yaml)).
+        :palm_tree: Nothing to do, AliECS natively supports generic commands. Make sure the task template for your command sets the control mode to `basic` ([see example](https://github.com/AliceO2Group/ControlWorkflows/blob/master/tasks/o2-roc-cleanup.yaml)).
 
 * I want to build and run AliECS for **development** purposes
 

docs/building.md

@@ -1,6 +1,6 @@
 # Building AliECS
 
-> **WARNING**: The building instructions described in this page are **for development purposes only**. Users interested in deploying, running and controlling O²/FLP software or their own software with AliECS should refer to the [O²/FLP Suite instructions](../../installation/) instead.
+> **WARNING**: The building instructions described in this page are **for development purposes only**. Users interested in deploying, running and controlling O²/FLP software or their own software with AliECS should refer to the [O²/FLP Suite instructions](https://alice-flp.docs.cern.ch/Operations/Experts/system-configuration/utils/o2-flp-setup/) instead.
 
 
 ## Overview
@@ -85,6 +85,6 @@ You should find several executables including `o2control-core`, `o2control-execu
 
 For subsequent builds (after the first one), plain `make` (instead of `make all`) is sufficient. See the [Makefile reference](makefile_reference.md) for more information.
 
-If you wish to also build the process control library and/or plugin, see [the OCC readme](./occ/README.md).
+If you wish to also build the process control library and/or plugin, see [the OCC readme](/occ/README.md).
 
-This build of AliECS can be run locally and connected to an existing O²/FLP Suite cluster by passing a `--mesosUrl` parameter. If you do this, remember to `systemctl stop o2-aliecs-core` on the head node, in order to stop the core that came with the O²/FLP Suite and use your own.
+This build of AliECS can be run locally and connected to an existing O²/FLP Suite cluster by passing a `--mesosUrl` parameter. If you do this, remember to `systemctl stop o2-aliecs-core` on the head node, in order to stop the core that came with the O²/FLP Suite and use your own.

docs/handbook/operation_order.md

@@ -4,7 +4,7 @@ This chapter attempts to document the order of important operations done during
 Since AliECS is an evolving system, the information presented here might be out-of-date, thus please refer to event handling in [core/environment/environment.go](https://github.com/AliceO2Group/Control/blob/master/core/environment/environment.go) and plugin calls in [ControlWorkflows/workflows/readout-dataflow.yaml](https://github.com/AliceO2Group/ControlWorkflows/blob/master/workflows/readout-dataflow.yaml) for the ultimate source of truth.
 Also, please report to the ECS developers any inaccuracies.
 
-[State Machine Callbacks](configuration.md#State-machine-callbacks) documents the order of callbacks that can be associated with state machine transitions.
+[State Machine Callbacks](configuration.md#state-machine-callbacks-moments) documents the order of callbacks that can be associated with state machine transitions.
 
 ## START_ACTIVITY (Start Of Run)
 

docs/handbook/overview.md

@@ -1,6 +1,6 @@
 # Design Overview
 
-AliECS in a distributed application, using Apache Mesos as toolkit. It integrates a task scheduler component, a purpose-built distributed state machine system, a multi-source stateful process configuration mechanism, and a control plugin and library compatible with any data-driven O2 process.
+AliECS is a distributed application, using Apache Mesos as toolkit. It integrates a task scheduler component, a purpose-built distributed state machine system, a multi-source stateful process configuration mechanism, and a control plugin and library compatible with any data-driven O2 process.
 
 ## AliECS Structure
 
@@ -25,7 +25,7 @@ Apache Mesos is a cluster resource management system. It greatly streamlines dis
 
 For AliECS, Mesos acts as an authoritative source of knowledge on the state of the cluster, as well as providing transport facilities for communication between the AliECS core and the executor.
 
-You can view the state of the cluster as presented by Mesos via the Mesos web interface, served on port `5050` of your head node when deployed via the [O²/FLP Suite setup tool](../../installation/).
+You can view the state of the cluster as presented by Mesos via the Mesos web interface, served on port `5050` of your head node when deployed via the O²/FLP Suite setup tool.
 
 
 ## FairMQ
@@ -40,4 +40,4 @@ The main state machine of AliECS is the environment state machine, which represe
 
 ![](AliECS-envsm.svg)
 
-While FairMQ devices use their own, FairMQ-specific state machine, non-FairMQ tasks based on the [OCC library](https://alice-flp-suite.docs.cern.ch/aliecs/occ/) use the same state machine as the AliECS environment state machine, the only difference being that the `START_ACTIVITY` transition is simply `START`, and the `STOP_ACTIVITY` transition is simply `STOP`.
+While FairMQ devices use their own, FairMQ-specific state machine, non-FairMQ tasks based on the [OCC library](/occ/README.md) use the same state machine as the AliECS environment state machine, the only difference being that the `START_ACTIVITY` transition is simply `START`, and the `STOP_ACTIVITY` transition is simply `STOP`.

docs/kafka.md

@@ -24,7 +24,7 @@ Once the topics exist, no further messages can be lost and no action is necessar
 
 ### Currently available topics
 
-See [events.proto](../common/protos/events.proto) for the protobuf definitions of the messages.
+See [events.proto](/common/protos/events.proto) for the protobuf definitions of the messages.
 
 * `aliecs.core` - core events that don't concern a specific environment or task
 * `aliecs.environment` - events that concern an environment, e.g. environment state changes
@@ -38,7 +38,7 @@ See [events.proto](../common/protos/events.proto) for the protobuf definitions o
 
 ### Decoding the messages
 
-Messages are encoded with protobuf, with the aforementioned [events.proto](../common/protos/events.proto) file defining the schema.
+Messages are encoded with protobuf, with the aforementioned [events.proto](/common/protos/events.proto) file defining the schema.
 Integraed service messages include a payload portion that is usually JSON-encoded, and has no predefined schema.
 
 To generate the precompiled protobuf interface, run `make fdset`.
@@ -79,7 +79,7 @@ As for today, AliECS publishes on the following types of topics:
 
 ### Decoding the messages
 
-Messages are encoded with protobuf. Please use [this](../core/integration/kafka/protos/kafka.proto) proto file to generate code which deserializes the messages.
+Messages are encoded with protobuf. Please use [this](/core/integration/kafka/protos/kafka.proto) proto file to generate code which deserializes the messages.
 
 ### Getting Start of Run and End of Run notifications
 

docs/running.md

@@ -1,7 +1,7 @@
 # Running AliECS as a developer
 
 
-> **WARNING**: The running instructions described in this page are **for development purposes only**. Users interested in deploying, running and controlling O²/FLP software or their own software with AliECS should refer to the [O²/FLP Suite instructions](https://alice-flp-suite.docs.cern.ch/installation/) instead.
+> **WARNING**: The running instructions described in this page are **for development purposes only**. Users interested in deploying, running and controlling O²/FLP software or their own software with AliECS should refer to the O²/FLP Suite instructions instead.
 
 
 ## Running the AliECS core
@@ -26,7 +26,7 @@ http://centosvmtest:5050/api/v1/scheduler
 --dumpWorkflows
 ```
 
-See [Using `coconut`](./coconut/README.md) for instructions on the O² Control core command line interface.
+See [Using `coconut`](/coconut/README.md) for instructions on the O² Control core command line interface.
 
 # Running AliECS in production
 

hacking/COG.md

@@ -44,11 +44,11 @@ In production, AliECS will manage and push all configuration to active tasks, bu
 
 Every task still has their own configuration file, with paths such as `/etc/flp.d/qc/*.json` for QualityControl and `/home/flp/readout.cfg` for Readout. These paths can be edited by the user, and any changes affect all newly launched instances of the task.
 
-All configuration file paths used by tasks can be found in the task descriptors of the workflow configuration repository in use. For more information on workflow configuration repositories, see [the `coconut repository` reference](https://github.com/AliceO2Group/Control/blob/doc/coconut/doc/coconut_repository.md). The default workflow configuration repository which comes pre-loaded with AliECS is accessible at [AliceO2Group/ControlWorkflows](https://github.com/AliceO2Group/ControlWorkflows) (all task descriptor files are found in the `tasks` directory).
+All configuration file paths used by tasks can be found in the task descriptors of the workflow configuration repository in use. For more information on workflow configuration repositories, see [the `coconut repository` reference](/coconut/doc/coconut_repository.md). The default workflow configuration repository which comes pre-loaded with AliECS is accessible at [AliceO2Group/ControlWorkflows](https://github.com/AliceO2Group/ControlWorkflows) (all task descriptor files are found in the `tasks` directory).
 
 * **modify an existing workflow or task?**
 
-You are free to keep as many workflow configuration repositories as you wish in your AliECS instance. For more information on workflow configuration repositories, see [the `coconut repository` reference](https://github.com/AliceO2Group/Control/blob/doc/coconut/doc/coconut_repository.md).
+You are free to keep as many workflow configuration repositories as you wish in your AliECS instance. For more information on workflow configuration repositories, see [the `coconut repository` reference](/coconut/doc/coconut_repository.md).
 
 Changes to a configuration repository are immediately available after running `coconut repo refresh`. There is no support in the AliECS GUI at this time.
 

occ/README.md

@@ -55,4 +55,4 @@ See [`peanut` Overview](peanut/README.md).
 
 ## OCC API debugging with `grpcc`
 
-See [OCC API debugging with `grpcc`](../docs/using_grpcc_occ.md).
+See [OCC API debugging with `grpcc`](/docs/using_grpcc_occ.md).

occ/occlib/examples/dummy-process/README.md

@@ -2,7 +2,7 @@
 
 This example is built from the top-level CMakeLists.txt when `BUILD_EXAMPLES` is true.
 
-For instructions on running it, see [Run example](../../../README.md#run-example).
+For instructions on running it, see [Run example](/occ/README.md#run-example).
 
 ## Standalone build