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diff --git a/docs/c/html/develop/igraph-Basic.html b/docs/c/html/develop/igraph-Basic.html
@@ -350,7 +350,7 @@ <h1 class="display-4">igraph Reference Manual</h1>
 in the above description should be distinguished from the mathematical
 definition of the empty or null graph. Strictly speaking, the empty or null
 graph in graph theory is the graph with no vertices and no edges. However
-by "empty graph" as used in <code class="constant">igraph</code> we mean a graph having zero or more
+by "empty graph" as used in <span class="command"><strong>igraph</strong></span> we mean a graph having zero or more
 vertices, but no edges.
 </p>
 <p><b>Arguments: </b>

diff --git a/docs/c/html/develop/igraph-Community.html b/docs/c/html/develop/igraph-Community.html
diff --git a/docs/c/html/develop/igraph-Data-structures.html b/docs/c/html/develop/igraph-Data-structures.html
diff --git a/docs/c/html/develop/igraph-Foreign.html b/docs/c/html/develop/igraph-Foreign.html
@@ -159,7 +159,6 @@ <h1 class="display-4">igraph Reference Manual</h1>
 <dt><span class="section"><a href="igraph-Foreign.html#graphviz-format">7. Graphviz format</a></span></dt>
 <dt><span class="section"><a href="igraph-Foreign.html#leda-format">8. LEDA format</a></span></dt>
 <dt><span class="section"><a href="igraph-Foreign.html#locale-helpers">9. Convenience functions for locale change</a></span></dt>
-<dt><span class="section"><a href="igraph-Foreign.html#deprecated-formats">10. Deprecated functions</a></span></dt>
 </dl></div>
 <p>These functions can write a graph to a file, or read a graph
 from a file.</p>
@@ -1137,7 +1136,7 @@ <h1 class="display-4">igraph Reference Manual</h1>
 <tbody><tr>
 <td><p><span class="term"><em class="parameter"><code></code></em></span></p></td>
 <td><p>
-  <a class="link" href="igraph-Foreign.html#igraph_write_graph_dimacs" title="10.2. igraph_write_graph_dimacs — Write a graph in DIMACS format (deprecated alias)."><code class="function">igraph_write_graph_dimacs()</code></a>
+  <a class="link" href="igraph-Foreign.html#igraph_write_graph_dimacs_flow" title="1.8. igraph_write_graph_dimacs_flow — Write a graph in DIMACS format."><code class="function">igraph_write_graph_dimacs_flow()</code></a>
   </p></td>
 </tr></tbody>
 </table></div>
@@ -3062,70 +3061,6 @@ <h3 class="title">Warning</h3>
 <p>
 
 
-</p>
-</div>
-</div>
-<div class="section">
-<div class="titlepage"><div><div><h2 class="title" style="clear: both">
-<a name="deprecated-formats"></a>10. Deprecated functions</h2></div></div></div>
-<div class="toc"><dl class="toc">
-<dt><span class="section"><a href="igraph-Foreign.html#igraph_read_graph_dimacs">10.1. <code class="function">igraph_read_graph_dimacs</code> —  Read a graph in DIMACS format (deprecated alias).</a></span></dt>
-<dt><span class="section"><a href="igraph-Foreign.html#igraph_write_graph_dimacs">10.2. <code class="function">igraph_write_graph_dimacs</code> —  Write a graph in DIMACS format (deprecated alias).</a></span></dt>
-</dl></div>
-<div class="section">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="igraph_read_graph_dimacs"></a>10.1. <code class="function">igraph_read_graph_dimacs</code> —  Read a graph in DIMACS format (deprecated alias).</h3></div></div></div>
-<a class="indexterm" name="id-1.22.14.2.2"></a><p>
-</p>
-<div class="informalexample"><pre class="programlisting">
-igraph_error_t igraph_read_graph_dimacs(igraph_t *graph, FILE *instream,
-                             igraph_strvector_t *problem,
-                             igraph_vector_int_t *label,
-                             igraph_integer_t *source,
-                             igraph_integer_t *target,
-                             igraph_vector_t *capacity,
-                             igraph_bool_t directed);
-</pre></div>
-<p>
-</p>
-<p>
-
-
-
-</p>
-<div class="warning" style="margin-left: 0.5in; margin-right: 0.5in;">
-<h3 class="title">Warning</h3>
-<p>Deprecated since version 0.10.0. Please do not use this function in new
-code; use <a class="link" href="igraph-Foreign.html#igraph_read_graph_dimacs_flow" title="1.7. igraph_read_graph_dimacs_flow — Read a graph in DIMACS format."><code class="function">igraph_read_graph_dimacs_flow()</code></a>
-instead.</p>
-</div>
-<p> 
-</p>
-</div>
-<div class="section">
-<div class="titlepage"><div><div><h3 class="title">
-<a name="igraph_write_graph_dimacs"></a>10.2. <code class="function">igraph_write_graph_dimacs</code> —  Write a graph in DIMACS format (deprecated alias).</h3></div></div></div>
-<a class="indexterm" name="id-1.22.14.3.2"></a><p>
-</p>
-<div class="informalexample"><pre class="programlisting">
-igraph_error_t igraph_write_graph_dimacs(const igraph_t *graph, FILE *outstream,
-                              igraph_integer_t source, igraph_integer_t target,
-                              const igraph_vector_t *capacity);
-</pre></div>
-<p>
-</p>
-<p>
-
-
-
-</p>
-<div class="warning" style="margin-left: 0.5in; margin-right: 0.5in;">
-<h3 class="title">Warning</h3>
-<p>Deprecated since version 0.10.0. Please do not use this function in new
-code; use <a class="link" href="igraph-Foreign.html#igraph_write_graph_dimacs_flow" title="1.8. igraph_write_graph_dimacs_flow — Write a graph in DIMACS format."><code class="function">igraph_write_graph_dimacs_flow()</code></a>
-instead.</p>
-</div>
-<p> 
 </p>
 </div>
 </div>

diff --git a/docs/c/html/develop/igraph-Generators.html b/docs/c/html/develop/igraph-Generators.html
@@ -1093,7 +1093,7 @@ <h1 class="display-4">igraph Reference Manual</h1>
 <td><p>
   Logical, for undirected graphs this specified
        whether each edge is included twice, in the vectors of
-       both adjacent vertices. If this is false (0), then it is
+       both adjacent vertices. If this is <code class="constant">false</code>, then it is
        assumed that every edge is included only once. This argument
        is ignored for directed graphs.
 </p></td>
@@ -1545,14 +1545,7 @@ <h1 class="display-4">igraph Reference Manual</h1>
 
 
 
-</p>
-<div class="warning" style="margin-left: 0.5in; margin-right: 0.5in;">
-<h3 class="title">Warning</h3>
-<p>This function is experimental and its signature is not considered final yet.
-We reserve the right to change the function signature without changing the
-major version of igraph. Use it at your own risk.</p>
-</div>
-<p>The hypercube graph <code class="constant">Q_n</code> has <code class="literal">2^n</code> vertices and
+The hypercube graph <code class="constant">Q_n</code> has <code class="literal">2^n</code> vertices and
 <code class="literal">2^(n-1) n</code> edges. Two vertices are connected when the binary
 representations of their zero-based vertex IDs differs in precisely one bit.
 
@@ -2159,7 +2152,7 @@ <h3 class="title">Warning</h3>
 </p>
 <p>
 Note that for <code class="literal">n=0</code>, the null graph is returned,
-which is not considered to be a tree by <a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree."><code class="function">igraph_is_tree()</code></a>.
+which is not considered to be a tree by <a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree."><code class="function">igraph_is_tree()</code></a>.
 
 </p>
 <p><b>Arguments: </b>
@@ -2292,10 +2285,10 @@ <h3 class="title">Warning</h3>
 <span class="emphasis"><em>       with edges pointing towards the root. */</em></span>
     <span class="strong"><strong><a class="link" href="igraph-Generators.html#igraph_kary_tree" title="1.15. igraph_kary_tree — Creates a k-ary tree in which almost all vertices have k children.">igraph_kary_tree</a></strong></span>(&amp;graph, 15, 2, IGRAPH_TREE_IN);
 
-    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_IN);
+    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_IN);
     <span class="strong"><strong>printf</strong></span>("Is it an in-tree? %s\n", res ? "Yes" : "No");
 
-    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_OUT);
+    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_OUT);
     <span class="strong"><strong>printf</strong></span>("Is it an out-tree? %s\n", res ? "Yes" : "No");
 
     <span class="strong"><strong><a class="link" href="igraph-Basic.html#igraph_destroy" title="4.1.4. igraph_destroy — Frees the memory allocated for a graph object.">igraph_destroy</a></strong></span>(&amp;graph);
@@ -2459,10 +2452,10 @@ <h3 class="title">Warning</h3>
 <span class="emphasis"><em>       with edges pointing towards the root. */</em></span>
     <span class="strong"><strong><a class="link" href="igraph-Generators.html#igraph_symmetric_tree" title="1.16. igraph_symmetric_tree — Creates a symmetric tree with the specified number of branches at each level.">igraph_symmetric_tree</a></strong></span>(&amp;graph, &amp;v, IGRAPH_TREE_IN);
 
-    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_IN);
+    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_IN);
     <span class="strong"><strong>printf</strong></span>("Is it an in-tree? %s\n", res ? "Yes" : "No");
 
-    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_OUT);
+    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;graph, &amp;res, NULL, IGRAPH_OUT);
     <span class="strong"><strong>printf</strong></span>("Is it an out-tree? %s\n", res ? "Yes" : "No");
 
     <span class="strong"><strong><a class="link" href="igraph-Basic.html#igraph_destroy" title="4.1.4. igraph_destroy — Frees the memory allocated for a graph object.">igraph_destroy</a></strong></span>(&amp;graph);
@@ -2627,7 +2620,7 @@ <h3 class="title">Warning</h3>
     <span class="strong"><strong><a class="link" href="igraph-Generators.html#igraph_regular_tree" title="1.17. igraph_regular_tree — Creates a regular tree.">igraph_regular_tree</a></strong></span>(&amp;tree, 4, 3, IGRAPH_TREE_UNDIRECTED);
 
     <span class="emphasis"><em>/* Bethe lattices are trees. */</em></span>
-    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;tree, &amp;is_tree, NULL, IGRAPH_ALL);
+    <span class="strong"><strong><a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree.">igraph_is_tree</a></strong></span>(&amp;tree, &amp;is_tree, NULL, IGRAPH_ALL);
     <span class="strong"><strong>printf</strong></span>("Is it a tree? %s\n", is_tree ? "Yes." : "No.");
 
     <span class="emphasis"><em>/* Compute and print eccentricities. The root is the most central. */</em></span>
@@ -2792,7 +2785,7 @@ <h3 class="title">Warning</h3>
 <td><p>
   <a class="link" href="igraph-Visitors.html#igraph_bfs" title="1.1. igraph_bfs — Breadth-first search."><code class="function">igraph_bfs()</code></a>, <a class="link" href="igraph-Visitors.html#igraph_bfs_simple" title="1.2. igraph_bfs_simple — Breadth-first search, single-source version"><code class="function">igraph_bfs_simple()</code></a> for back-conversion;
 <a class="link" href="igraph-Generators.html#igraph_from_prufer" title="1.28. igraph_from_prufer — Generates a tree from a Prüfer sequence."><code class="function">igraph_from_prufer()</code></a> for creating trees from Prüfer sequences;
-<a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree."><code class="function">igraph_is_tree()</code></a> and <a class="link" href="igraph-Structural.html#igraph_is_forest" title="15.6. igraph_is_forest — Decides whether the graph is a forest."><code class="function">igraph_is_forest()</code></a> to check if a graph
+<a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree."><code class="function">igraph_is_tree()</code></a> and <a class="link" href="igraph-Structural.html#igraph_is_forest" title="15.4. igraph_is_forest — Decides whether the graph is a forest."><code class="function">igraph_is_forest()</code></a> to check if a graph
 is a tree or forest.
   </p></td>
 </tr></tbody>
@@ -4569,7 +4562,7 @@ <h3 class="title">Warning</h3>
 <tbody><tr>
 <td><p><span class="term"><em class="parameter"><code></code></em></span></p></td>
 <td><p>
-  <a class="link" href="igraph-Structural.html#igraph_to_prufer" title="15.7. igraph_to_prufer — Converts a tree to its Prüfer sequence."><code class="function">igraph_to_prufer()</code></a>, <a class="link" href="igraph-Generators.html#igraph_kary_tree" title="1.15. igraph_kary_tree — Creates a k-ary tree in which almost all vertices have k children."><code class="function">igraph_kary_tree()</code></a>, <a class="link" href="igraph-Generators.html#igraph_tree_game" title="2.30. igraph_tree_game — Generates a random tree with the given number of nodes."><code class="function">igraph_tree_game()</code></a>
+  <a class="link" href="igraph-Structural.html#igraph_to_prufer" title="15.5. igraph_to_prufer — Converts a tree to its Prüfer sequence."><code class="function">igraph_to_prufer()</code></a>, <a class="link" href="igraph-Generators.html#igraph_kary_tree" title="1.15. igraph_kary_tree — Creates a k-ary tree in which almost all vertices have k children."><code class="function">igraph_kary_tree()</code></a>, <a class="link" href="igraph-Generators.html#igraph_tree_game" title="2.30. igraph_tree_game — Generates a random tree with the given number of nodes."><code class="function">igraph_tree_game()</code></a>
   </p></td>
 </tr></tbody>
 </table></div>
@@ -9722,7 +9715,7 @@ <h3 class="title">Warning</h3>
 </p>
 <p>
 Note that for <code class="literal">n=0</code>, the null graph is returned,
-which is not considered to be a tree by <a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.5. igraph_is_tree — Decides whether the graph is a tree."><code class="function">igraph_is_tree()</code></a>.
+which is not considered to be a tree by <a class="link" href="igraph-Structural.html#igraph_is_tree" title="15.3. igraph_is_tree — Decides whether the graph is a tree."><code class="function">igraph_is_tree()</code></a>.
 
 </p>
 <p><b>Arguments: </b>