Fix links not to point to .html - .md is right, else the non-html generators won't work properly.

Documentation/Books/Users/Glossary/README.mdpp

@@ -91,7 +91,7 @@ This behavior can be changed on a per-collection level by creating collections w
 
 Using `keyOptions` it is possible to disallow user-specified keys completely, or to force a specific regime for auto-generating the `_key` values.
 
-There are some restrictions for user-defined keys (see [NamingConventions for document keys](../NamingConventions/DocumentKeys.html).
+There are some restrictions for user-defined keys (see [NamingConventions for document keys](../NamingConventions/DocumentKeys.md).
 
 !SUBSECTION Document Revision
 

arangod/V8Server/v8-vocindex.cpp

@@ -1153,7 +1153,7 @@ static void CreateCollectionCoordinator (const v8::FunctionCallbackInfo<v8::Valu
 /// **sparse** can be *true* or *false*.
 ///
 /// For *hash*, and *skiplist* the sparsity can be controlled, *fulltext* and *geo*
-/// are [sparse](WhichIndex.html) by definition.
+/// are [sparse](WhichIndex.md) by definition.
 ///
 /// **unique** can be *true* or *false* and is supported by *hash* or *skiplist*
 ///

js/actions/api-explain.js

@@ -96,7 +96,7 @@ var ERRORS = require("internal").errors;
 /// 
 /// Each plan in the result is a JSON object with the following attributes:
 /// - *nodes*: the array of execution nodes of the plan. The array of available node types
-///   can be found [here](../Aql/Optimizer.html)
+///   can be found [here](../Aql/Optimizer.md)
 ///
 /// - *estimatedCost*: the total estimated cost for the plan. If there are multiple
 ///   plans, the optimizer will choose the plan with the lowest total cost.
@@ -104,7 +104,7 @@ var ERRORS = require("internal").errors;
 /// - *collections*: an array of collections used in the query
 ///
 /// - *rules*: an array of rules the optimizer applied. An overview of the
-///   available rules can be found [here](../Aql/Optimizer.html)
+///   available rules can be found [here](../Aql/Optimizer.md)
 ///
 /// - *variables*: array of variables used in the query (note: this may contain
 ///   internal variables created by the optimizer)

js/apps/system/_api/gharial/APP/gharial.js

@@ -274,7 +274,7 @@
 /// @RESTRETURNCODE{409}
 /// Returned if there is a conflict storing the graph.
 /// This can occur either if a graph with this name is already stored, or if there is one edge definition with a
-/// the same [edge collection](../Glossary/index.html#edge-collection)
+/// the same [edge collection](../Glossary/README.md#edge-collection)
 /// but a different signature used in any other graph.
 /// 
 /// @EXAMPLES
@@ -1629,7 +1629,7 @@
 /// Creates a new edge in the collection.
 /// Within the body the has to contain a *\_from* and *\_to* value referencing to valid vertices in the graph.
 /// Furthermore the edge has to be valid in the definition of this
-/// [edge collection](../Glossary/index.html#edge-collection).
+/// [edge collection](../Glossary/README.md#edge-collection).
 /// 
 /// @RESTURLPARAMETERS
 /// 

js/server/modules/org/arangodb/cluster/kickstarter.js

@@ -1021,13 +1021,13 @@ function Kickstarter (clusterPlan, myname) {
 /// itself. We do not go into details here about the data structure,
 /// but the most important information are the process IDs of the
 /// started processes. The corresponding
-/// [see shutdown method](../ModulePlanner/#shutdown) needs this 
+/// [see shutdown method](../ModulePlanner/README.md#shutdown) needs this 
 /// information to shut down all processes.
 ///
 /// Note that all data in the DBservers and all log files and all agency
 /// information in the cluster is deleted by this call. This is because
 /// it is intended to set up a cluster for the first time. See
-/// the [relaunch method](../ModulePlanner/#relaunch)
+/// the [relaunch method](../ModulePlanner/README.md#relaunch)
 /// for restarting a cluster without data loss.
 /// @endDocuBlock
 ////////////////////////////////////////////////////////////////////////////////
@@ -1121,12 +1121,12 @@ Kickstarter.prototype.launch = function () {
 /// itself. We do not go into details here about the data structure,
 /// but the most important information are the process IDs of the
 /// started processes. The corresponding
-/// [shutdown method ](../ModulePlanner/#shutdown) needs this information to
+/// [shutdown method ](../ModulePlanner/README.md#shutdown) needs this information to
 /// shut down all processes.
 ///
 /// Note that this methods needs that all data in the DBservers and the
 /// agency information in the cluster are already set up properly. See
-/// the [launch method](../ModulePlanner/#launch) for
+/// the [launch method](../ModulePlanner/README.md#launch) for
 /// starting a cluster for the first time.
 /// @endDocuBlock
 ////////////////////////////////////////////////////////////////////////////////
@@ -1303,7 +1303,7 @@ Kickstarter.prototype.shutdown = function() {
 ///
 /// This cleans up all the data and logs of a previously shut down cluster.
 /// To this end, other dispatchers are contacted as necessary.
-/// [Use shutdown](../ModulePlanner/#shutdown) first and
+/// [Use shutdown](../ModulePlanner/README.md#shutdown) first and
 /// use with caution, since potentially a lot of data is being erased with
 /// this call!
 /// @endDocuBlock
@@ -1490,12 +1490,12 @@ Kickstarter.prototype.isHealthy = function() {
 /// itself. We do not go into details here about the data structure,
 /// but the most important information are the process IDs of the
 /// started processes. The corresponding
-/// [shutdown method](../ModulePlanner/#shutdown) needs
+/// [shutdown method](../ModulePlanner/README.md#shutdown) needs
 /// this information to shut down all processes.
 ///
 /// Note that this methods needs that all data in the DBservers and the
 /// agency information in the cluster are already set up properly. See
-/// the [launch method](../ModulePlanner/#launch) for
+/// the [launch method](../ModulePlanner/README.md#launch) for
 /// starting a cluster for the first time.
 /// @endDocuBlock
 ////////////////////////////////////////////////////////////////////////////////