Fix buttons on the PaSiMap plot window

[jalview.git] / help / help / html / features / clarguments-basic.html

diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html
index edee480..7a87602 100644 (file)
--- a/help/help/html/features/clarguments-basic.html
+++ b/help/help/html/features/clarguments-basic.html
@@ -25,15 +25,15 @@
   <h1>Command Line: basic usage</h1>
 
   <p>
-  <a href="clarguments.html">Command Line: summary</a>
-  <br/>
-  <a href="clarguments-intro.html">Command Line: introduction</a>
+  <a href="clarguments.html">Command Line: introduction</a>
   <br/>
   Command Line: basic usage
   <br/>
   <a href="clarguments-advanced.html">Command Line: advanced usage</a>
   <br/>
   <a href="clarguments-argfiles.html">Command Line: argument files</a>
+  <br/>
+  <a href="clarguments-reference.html">Command Line: reference</a>
   </p>
 
   <hr/>
@@ -408,6 +408,10 @@
   </pre>
   </p>
 
+  <p>
+  <em>Important!</em> If you use <code>--output</code> or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified <code>--headless</code>).  To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> or <code>--noheadless</code> argument (the order doesn't matter).
+  </p>
+
   <h3><a name="format"></a><code>--format</code></h3>
 
   <p>
@@ -655,8 +659,7 @@
   <hr/>
   Continue to <a href="clarguments-advanced.html">Command Line: advanced usage</a>.
   <br/>
-  Return to <a href="clarguments.html">Command Line: summary</a>.
-
+  <a href="clarguments-reference.html">Command Line: reference</a>
 
 </body>
 </html>