diff --git a/java/server/src/main/java/org/softwareheritage/graph/AllowedEdges.java b/java/server/src/main/java/org/softwareheritage/graph/AllowedEdges.java
--- a/java/server/src/main/java/org/softwareheritage/graph/AllowedEdges.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/AllowedEdges.java
@@ -7,6 +7,11 @@
 
 /**
  * Edge restriction based on node types, used when visiting the graph.
+ * <p>
+ * <a href="https://docs.softwareheritage.org/devel/swh-model/data-model.html">Software Heritage
+ * graph</a> contains multiple node types (contents, directories, revisions, ...) and restricting
+ * the traversal to specific node types is necessary for many querying operations: <a
+ * href="https://docs.softwareheritage.org/devel/swh-graph/use-cases.html">use cases</a>.
  *
  * @author Thibault Allançon
  * @version 0.0.1
@@ -27,7 +32,8 @@
    * Constructor.
    *
    * @param graph the graph on which to perform edge restriction
-   * @param edgesFmt a formatted string describing allowed edges (TODO: link API doc)
+   * @param edgesFmt a formatted string describing <a
+   * href="https://docs.softwareheritage.org/devel/swh-graph/api.html#terminology">allowed edges</a>
    */
   public AllowedEdges(Graph graph, String edgesFmt) {
     this.graph = graph;
@@ -45,7 +51,6 @@
     }
 
     // Format: "src1:dst1,src2:dst2,[...]"
-    // TODO: link API doc
     String[] edgeTypes = edgesFmt.split(",");
     for (String edgeType : edgeTypes) {
       String[] nodeTypes = edgeType.split(":");
diff --git a/java/server/src/main/java/org/softwareheritage/graph/App.java b/java/server/src/main/java/org/softwareheritage/graph/App.java
--- a/java/server/src/main/java/org/softwareheritage/graph/App.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/App.java
@@ -23,7 +23,7 @@
 import org.softwareheritage.graph.algo.Stats;
 
 /**
- * Entrypoint of the swh-graph server REST API.
+ * Web framework of the swh-graph server REST API.
  *
  * @author Thibault Allançon
  * @version 0.0.1
@@ -31,6 +31,11 @@
  */
 
 public class App {
+  /**
+   * Main entrypoint.
+   *
+   * @param args command line arguments
+   */
   public static void main(String[] args) throws IOException, JSAPException {
     SimpleJSAP jsap = new SimpleJSAP(
         App.class.getName(),
@@ -54,6 +59,12 @@
     startServer(graphPath, port);
   }
 
+  /**
+   * Loads compressed graph and starts the web server to query it.
+   *
+   * @param graphPath basename of the compressed graph
+   * @param port binding port of the server
+   */
   private static void startServer(String graphPath, int port) throws IOException {
     Graph graph = new Graph(graphPath);
     Stats stats = new Stats(graphPath);
@@ -140,6 +151,13 @@
     });
   }
 
+  /**
+   * Checks query strings names provided to the REST API.
+   *
+   * @param ctx Javalin HTTP request context
+   * @param allowedFmt a regular expression describing allowed query strings names
+   * @throws IllegalArgumentException unknown query string provided
+   */
   private static void checkQueryStrings(Context ctx, String allowedFmt) {
     Map<String, List<String>> queryParamMap = ctx.queryParamMap();
     for (String key : queryParamMap.keySet()) {
diff --git a/java/server/src/main/java/org/softwareheritage/graph/Endpoint.java b/java/server/src/main/java/org/softwareheritage/graph/Endpoint.java
--- a/java/server/src/main/java/org/softwareheritage/graph/Endpoint.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/Endpoint.java
@@ -13,10 +13,15 @@
 
 /**
  * REST API endpoints wrapper functions.
+ * <p>
+ * Graph operations are segmented between high-level class (this one) and the low-level class
+ * ({@link Traversal}). The {@link Endpoint} class creates wrappers for each endpoints by performing
+ * all the input/output node ids conversions and logging timings.
  *
  * @author Thibault Allançon
  * @version 0.0.1
  * @since 0.0.1
+ * @see org.softwareheritage.graph.algo.Traversal
  */
 
 public class Endpoint {
@@ -33,7 +38,8 @@
    *
    * @param graph the graph used for traversal endpoint
    * @param direction a string (either "forward" or "backward") specifying edge orientation
-   * @param edgesFmt a formatted string describing allowed edges (TODO: link API doc)
+   * @param edgesFmt a formatted string describing <a
+   * href="https://docs.softwareheritage.org/devel/swh-graph/api.html#terminology">allowed edges</a>
    */
   public Endpoint(Graph graph, String direction, String edgesFmt) {
     this.graph = graph;
@@ -94,10 +100,10 @@
   }
 
   /**
-   * Leaves endpoint wrapper (performs input/output node ids conversions).
+   * Leaves endpoint wrapper.
    *
-   * @param src source node of endpoint call specified as a SwhId
-   * @return the resulting list of SwhId from endpoint call
+   * @param src source node of endpoint call specified as a {@link SwhId}
+   * @return the resulting list of {@link SwhId} from endpoint call
    * @see org.softwareheritage.graph.SwhId
    * @see org.softwareheritage.graph.algo.Traversal#leaves(long)
    */
@@ -113,10 +119,10 @@
   }
 
   /**
-   * Neighbors endpoint wrapper (performs input/output node ids conversions).
+   * Neighbors endpoint wrapper.
    *
-   * @param src source node of endpoint call specified as a SwhId
-   * @return the resulting list of SwhId from endpoint call
+   * @param src source node of endpoint call specified as a {@link SwhId}
+   * @return the resulting list of {@link SwhId} from endpoint call
    * @see org.softwareheritage.graph.SwhId
    * @see org.softwareheritage.graph.algo.Traversal#neighbors(long)
    */
@@ -132,10 +138,11 @@
   }
 
   /**
-   * Walk endpoint wrapper (performs input/output node ids conversions).
+   * Walk endpoint wrapper.
    *
-   * @param src source node of endpoint call specified as a SwhId
-   * @param dstFmt destination used in endpoint call (TODO: link to API doc)
+   * @param src source node of endpoint call specified as a {@link SwhId}
+   * @param dstFmt destination formatted string as described in the <a
+   * href="https://docs.softwareheritage.org/devel/swh-graph/api.html#walk">API</a>
    * @param algorithm traversal algorithm used in endpoint call (either "dfs" or "bfs")
    * @return the resulting {@link SwhPath} from endpoint call
    * @see org.softwareheritage.graph.SwhId
@@ -170,10 +177,10 @@
   }
 
   /**
-   * VisitNodes endpoint wrapper (performs input/output node ids conversions).
+   * VisitNodes endpoint wrapper.
    *
-   * @param src source node of endpoint call specified as a SwhId
-   * @return the resulting list of SwhId from endpoint call
+   * @param src source node of endpoint call specified as a {@link SwhId}
+   * @return the resulting list of {@link SwhId} from endpoint call
    * @see org.softwareheritage.graph.SwhId
    * @see org.softwareheritage.graph.algo.Traversal#visitNodes(long)
    */
@@ -189,9 +196,9 @@
   }
 
   /**
-   * VisitPaths endpoint wrapper (performs input/output node ids conversions).
+   * VisitPaths endpoint wrapper.
    *
-   * @param src source node of endpoint call specified as a SwhId
+   * @param src source node of endpoint call specified as a {@link SwhId}
    * @return the resulting list of {@link SwhPath} from endpoint call
    * @see org.softwareheritage.graph.SwhId
    * @see org.softwareheritage.graph.SwhPath
diff --git a/java/server/src/main/java/org/softwareheritage/graph/Graph.java b/java/server/src/main/java/org/softwareheritage/graph/Graph.java
--- a/java/server/src/main/java/org/softwareheritage/graph/Graph.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/Graph.java
@@ -11,10 +11,22 @@
 
 /**
  * Main class storing the compressed graph and node id mappings.
+ * <p>
+ * The compressed graph is stored using the <a href="http://webgraph.di.unimi.it/">WebGraph</a>
+ * ecosystem. Additional mappings are necessary because Software Heritage uses string based <a
+ * href="https://docs.softwareheritage.org/devel/swh-model/persistent-identifiers.html">persistent
+ * identifiers</a> (PID) while WebGraph uses integers internally. These two mappings (long id &harr;
+ * PID) are used for the input (users refer to the graph using PID) and the output (convert back to
+ * PID for users results). However, since graph traversal can be restricted depending on the node
+ * type (see {@link AllowedEdges}), a long id &rarr; node type map is stored as well to avoid a full
+ * PID lookup.
  *
  * @author Thibault Allançon
  * @version 0.0.1
  * @since 0.0.1
+ * @see org.softwareheritage.graph.AllowedEdges
+ * @see org.softwareheritage.graph.NodeIdMap;
+ * @see org.softwareheritage.graph.NodeTypesMap;
  */
 
 public class Graph {
@@ -120,8 +132,8 @@
    * Returns list of successors of a node.
    *
    * @param nodeId node specified as a long id
-   * @return list of successors of the node, specified as a {@link LongBigArrays}
-   * @see it.unimi.dsi.fastutil.longs.LongBigArrays
+   * @return list of successors of the node, specified as a <a
+   * href="http://fastutil.di.unimi.it/">fastutil</a> LongBigArrays
    */
   public long[][] successors(long nodeId) {
     return graph.successorBigArray(nodeId);
@@ -141,8 +153,8 @@
    * Returns list of predecessors of a node.
    *
    * @param nodeId node specified as a long id
-   * @return list of predecessors of the node, specified as a {@link LongBigArrays}
-   * @see it.unimi.dsi.fastutil.longs.LongBigArrays
+   * @return list of successors of the node, specified as a <a
+   * href="http://fastutil.di.unimi.it/">fastutil</a> LongBigArrays
    */
   public long[][] predecessors(long nodeId) {
     return graphTransposed.successorBigArray(nodeId);
@@ -174,8 +186,8 @@
    *
    * @param nodeId node specified as a long id
    * @param useTransposed boolean value to use transposed graph
-   * @return list of neighbors of the node, specified as a {@link LongBigArrays}
-   * @see it.unimi.dsi.fastutil.longs.LongBigArrays
+   * @return list of successors of the node, specified as a <a
+   * href="http://fastutil.di.unimi.it/">fastutil</a> LongBigArrays
    */
   public long[][] neighbors(long nodeId, boolean useTransposed) {
     return (useTransposed) ? predecessors(nodeId) : successors(nodeId);
diff --git a/java/server/src/main/java/org/softwareheritage/graph/Neighbors.java b/java/server/src/main/java/org/softwareheritage/graph/Neighbors.java
--- a/java/server/src/main/java/org/softwareheritage/graph/Neighbors.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/Neighbors.java
@@ -9,10 +9,13 @@
 
 /**
  * Iterator class to go over a node neighbors in the graph.
+ * <p>
+ * Wrapper iterator class to easily deal with {@link AllowedEdges} during traversals.
  *
  * @author Thibault Allançon
  * @version 0.0.1
  * @since 0.0.1
+ * @see org.softwareheritage.graph.AllowedEdges
  */
 
 public class Neighbors implements Iterable<Long> {
@@ -56,6 +59,7 @@
   public class NeighborsIterator implements Iterator<Long> {
     long nextNeighborIdx;
     long nbNeighbors;
+    // LongBigArrays to support 64-bit indexing.
     long[][] neighbors;
 
     public NeighborsIterator() {
@@ -65,7 +69,7 @@
     }
 
     public boolean hasNext() {
-      // No edge restriction case: bypass type checks and skip to next neighbor
+      // Case 1: no edge restriction, bypass type checks and skip to next neighbor
       if (edges.restrictedTo == null) {
         if (nextNeighborIdx + 1 < nbNeighbors) {
           nextNeighborIdx++;
@@ -75,7 +79,7 @@
         }
       }
 
-      // Edge restriction case: look ahead for next neighbor
+      // Case 2: edge restriction, look ahead for next neighbor
       for (long lookAheadIdx = nextNeighborIdx + 1; lookAheadIdx < nbNeighbors; lookAheadIdx++) {
         long nextNodeId = LongBigArrays.get(neighbors, lookAheadIdx);
         if (edges.isAllowed(srcNodeId, nextNodeId)) {
diff --git a/java/server/src/main/java/org/softwareheritage/graph/Node.java b/java/server/src/main/java/org/softwareheritage/graph/Node.java
--- a/java/server/src/main/java/org/softwareheritage/graph/Node.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/Node.java
@@ -57,7 +57,7 @@
     }
 
     /**
-     * Parses SWH node type from string.
+     * Converts string to corresponding SWH node type.
      *
      * @param strType node type represented as a string
      * @return the corresponding {@link Node.Type} value
@@ -71,9 +71,11 @@
     }
 
     /**
-     * Parses SWH node type possible values from formatted string (TODO: link API doc).
+     * Parses SWH node type possible values from formatted string (see the <a
+     * href="https://docs.softwareheritage.org/devel/swh-graph/api.html#terminology">API
+     * syntax</a>).
      *
-     * @param strFmtType node types represented as a formatted string (TODO: link API doc)
+     * @param strFmtType node types represented as a formatted string
      * @return a list containing the {@link Node.Type} values
      * @see org.softwareheritage.graph.Node.Type
      */
diff --git a/java/server/src/main/java/org/softwareheritage/graph/SwhPath.java b/java/server/src/main/java/org/softwareheritage/graph/SwhPath.java
--- a/java/server/src/main/java/org/softwareheritage/graph/SwhPath.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/SwhPath.java
@@ -16,6 +16,7 @@
  */
 
 public class SwhPath {
+  /** Internal list of {@link SwhId} */
   ArrayList<SwhId> path;
 
   /**
@@ -40,7 +41,7 @@
   /**
    * Constructor.
    *
-   * @param swhIds variable number of @{link SwhId} to initialize this path with
+   * @param swhIds variable number of {@link SwhId} to initialize this path with
    * @see org.softwareheritage.graph.SwhId
    */
   public SwhPath(SwhId ...swhIds) {
diff --git a/java/server/src/main/java/org/softwareheritage/graph/algo/Stats.java b/java/server/src/main/java/org/softwareheritage/graph/algo/Stats.java
--- a/java/server/src/main/java/org/softwareheritage/graph/algo/Stats.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/algo/Stats.java
@@ -6,6 +6,9 @@
 
 /**
  * Statistics on the compressed graph.
+ * <p>
+ * These statistics are not computed but directly read from <a
+ * href="http://webgraph.di.unimi.it/">WebGraph</a> generated .stats and .properties files.
  *
  * @author Thibault Allançon
  * @version 0.0.1
@@ -39,7 +42,7 @@
   /**
    * Constructor.
    *
-   * @param graphPath full path of compressed graph
+   * @param graphPath path and basename of compressed graph
    */
   public Stats(String graphPath) throws IOException {
     Properties properties = new Properties();
diff --git a/java/server/src/main/java/org/softwareheritage/graph/algo/Traversal.java b/java/server/src/main/java/org/softwareheritage/graph/algo/Traversal.java
--- a/java/server/src/main/java/org/softwareheritage/graph/algo/Traversal.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/algo/Traversal.java
@@ -10,16 +10,22 @@
 import it.unimi.dsi.fastutil.longs.LongBigArrays;
 
 import org.softwareheritage.graph.AllowedEdges;
+import org.softwareheritage.graph.Endpoint;
 import org.softwareheritage.graph.Graph;
 import org.softwareheritage.graph.Neighbors;
 import org.softwareheritage.graph.Node;
 
 /**
  * Traversal algorithms on the compressed graph.
+ * <p>
+ * Internal implementation of the traversal API endpoints. These methods only input/output internal
+ * long ids, which are converted in the {@link Endpoint} higher-level class to Software Heritage
+ * PID.
  *
  * @author Thibault Allançon
  * @version 0.0.1
  * @since 0.0.1
+ * @see org.softwareheritage.graph.Endpoint
  */
 
 public class Traversal {
@@ -30,15 +36,9 @@
   /** Graph edge restriction */
   AllowedEdges edges;
 
-  /**
-   * Bit array storing if we have visited a node
-   * @see it.unimi.dsi.bits.LongArrayBitVector
-   */
+  /** Bit array storing if we have visited a node */
   LongArrayBitVector visited;
-  /**
-   * Array storing parent node id for each nodes during a traversal
-   * @see it.unimi.dsi.fastutil.longs.LongBigArrays
-   */
+  /** LongBigArray storing parent node id for each nodes during a traversal */
   long[][] nodeParent;
 
   /**
@@ -46,7 +46,8 @@
    *
    * @param graph graph used in the traversal
    * @param direction a string (either "forward" or "backward") specifying edge orientation
-   * @param edgesFmt a formatted string describing allowed edges (TODO: link API doc)
+   * @param edgesFmt a formatted string describing <a
+   * href="https://docs.softwareheritage.org/devel/swh-graph/api.html#terminology">allowed edges</a>
    */
   public Traversal(Graph graph, String direction, String edgesFmt) {
     if (!direction.matches("forward|backward")) {
diff --git a/java/server/src/main/java/org/softwareheritage/graph/backend/MapFile.java b/java/server/src/main/java/org/softwareheritage/graph/backend/MapFile.java
--- a/java/server/src/main/java/org/softwareheritage/graph/backend/MapFile.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/backend/MapFile.java
@@ -9,6 +9,10 @@
 
 /**
  * Wrapper class around very big mmap()-ed file.
+ * <p>
+ * Java has a limit for mmap()-ed files because of unsupported 64-bit indexing. The <a
+ * href="http://dsiutils.di.unimi.it/">dsiutils</a> ByteBufferInputStream is used to overcome this
+ * Java limit.
  *
  * @author Thibault Allançon
  * @version 0.0.1
@@ -16,10 +20,7 @@
  */
 
 public class MapFile {
-  /**
-   * Memory-mapped file buffer
-   * @see it.unimi.dsi.io.ByteBufferInputStream
-   */
+  /** Memory-mapped file buffer */
   ByteBufferInputStream bufferMap;
   /** Fixed line length of the mmap()-ed file */
   int lineLength;
diff --git a/java/server/src/main/java/org/softwareheritage/graph/backend/NodeIdMap.java b/java/server/src/main/java/org/softwareheritage/graph/backend/NodeIdMap.java
--- a/java/server/src/main/java/org/softwareheritage/graph/backend/NodeIdMap.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/backend/NodeIdMap.java
@@ -5,13 +5,18 @@
 import org.softwareheritage.graph.Graph;
 import org.softwareheritage.graph.SwhId;
 import org.softwareheritage.graph.backend.MapFile;
+import org.softwareheritage.graph.backend.Setup;
 
 /**
  * Mapping between internal long node id and external SWH PID.
+ * <p>
+ * Mappings in both directions are pre-computed and dumped on disk in the {@link Setup} class, then
+ * they are loaded here using mmap().
  *
  * @author Thibault Allançon
  * @version 0.0.1
  * @since 0.0.1
+ * @see org.softwareheritage.graph.backend.Setup
  */
 
 public class NodeIdMap {
@@ -20,7 +25,7 @@
   /** Fixed length of long node id */
   public static final int NODE_ID_LENGTH = 20;
 
-  /** Full graph path */
+  /** Graph path and basename */
   String graphPath;
   /** Number of ids to map */
   long nbIds;
diff --git a/java/server/src/main/java/org/softwareheritage/graph/backend/NodeTypesMap.java b/java/server/src/main/java/org/softwareheritage/graph/backend/NodeTypesMap.java
--- a/java/server/src/main/java/org/softwareheritage/graph/backend/NodeTypesMap.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/backend/NodeTypesMap.java
@@ -11,6 +11,11 @@
 /**
  * Mapping between long node id and SWH node type as described in the <a
  * href="https://docs.softwareheritage.org/devel/swh-model/data-model.html">data model</a>.
+ * <p>
+ * The type mapping is pre-computed and dumped on disk in the {@link Setup} class, then it is loaded
+ * in-memory here using <a href="http://fastutil.di.unimi.it/">fastutil</a> LongBigList. To be
+ * space-efficient, the mapping is stored as a bitmap using minimum number of bits per {@link
+ * Node.Type}.
  *
  * @author Thibault Allançon
  * @version 0.0.1
@@ -18,16 +23,13 @@
  */
 
 public class NodeTypesMap {
-  /**
-   * Array storing for each node its type
-   * @see it.unimi.dsi.fastutil.longs.LongBigList
-   */
+  /** Array storing for each node its type */
   LongBigList nodeTypesMap;
 
   /**
    * Constructor.
    *
-   * @param graphPath full path of the compressed graph
+   * @param graphPath path and basename of the compressed graph
    */
   public NodeTypesMap(String graphPath) throws IOException {
     try {
diff --git a/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java b/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java
--- a/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/backend/Setup.java
@@ -33,6 +33,11 @@
  */
 
 public class Setup {
+  /**
+   * Main entrypoint.
+   *
+   * @param args command line arguments
+   */
   public static void main(String[] args) throws IOException {
     if (args.length != 2) {
       System.err.println("Expected parameters: <nodes.csv.gz path> <compressed graph path>");
diff --git a/java/server/src/main/java/org/softwareheritage/graph/benchmark/LinuxLog.java b/java/server/src/main/java/org/softwareheritage/graph/benchmark/LinuxLog.java
--- a/java/server/src/main/java/org/softwareheritage/graph/benchmark/LinuxLog.java
+++ b/java/server/src/main/java/org/softwareheritage/graph/benchmark/LinuxLog.java
@@ -8,6 +8,9 @@
 
 /**
  * Linux git log experiment to benchmark graph traversal.
+ * <p>
+ * The goal is to do the equivalent of a {@code git log} in the Linux kernel by following revisions
+ * nodes.
  *
  * @author Thibault Allançon
  * @version 0.0.1
@@ -15,6 +18,11 @@
  */
 
 public class LinuxLog {
+  /**
+   * Main entrypoint.
+   *
+   * @param args command line arguments
+   */
   public static void main(String[] args) throws IOException {
     String path = args[0];
     Graph graph = new Graph(path);