diff --git a/.gitignore b/.gitignore
index 844fd863a1f3c9e1e59df8be77b0f7e2ea58ca7e..793db8febb9d5c06fee031ba097082c98010fa57 100644
--- a/.gitignore
+++ b/.gitignore
@@ -37,8 +37,8 @@ config.log
*.pcm
\#*\#
-# THtml generated documentation directory
-docs/htmldoc
+# Doxygen generated documentation directory
+docs/html
# Examples directory
examples/*.root
diff --git a/Doxyfile b/docs/Doxyfile
similarity index 99%
rename from Doxyfile
rename to docs/Doxyfile
index 08e960e33fb1dc76f406f826b2a66fe0493e0f96..04f04c11ec75e74f95bb9848cac6e7af4c442c32 100644
--- a/Doxyfile
+++ b/docs/Doxyfile
@@ -41,7 +41,7 @@ PROJECT_NUMBER =
# If a relative path is entered, it will be relative to the location
# where doxygen was started. If left blank the current directory will be used.
-OUTPUT_DIRECTORY = ../doxygen_output
+OUTPUT_DIRECTORY = $(DOXYGEN_OUTPUT_DIRECTORY)
# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
# 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -571,7 +571,7 @@ WARN_LOGFILE =
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
-INPUT = README.md podd/src podd/hana_decode src
+INPUT = ../README.md ../src ../podd/src ../podd/hana_decode
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..68b3aa7a5602036f1e894172fa003e1fdcec30a0
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,14 @@
+.PHONY: doxygen clean
+
+DOXYGEN_OUTPUT_DIRECTORY ?= .
+export DOXYGEN_OUTPUT_DIRECTORY
+export DOXYGEN_SOURCE_DIRECTORY := ..
+
+
+all: doxygen
+
+doxygen:
+ doxygen
+
+clean:
+ rm -r $(DOXYGEN_OUTPUT_DIRECTORY)/html
diff --git a/docs/doc_footer.html b/docs/doc_footer.html
deleted file mode 100755
index 2f394e0d01a9e510b96c79abc1e526e75f44c9ae..0000000000000000000000000000000000000000
--- a/docs/doc_footer.html
+++ /dev/null
@@ -1,10 +0,0 @@
-<br />
-<!--SIGNATURE-->
-<div id="footer">
-<em>» Author: %AUTHOR% </em><em>» Copyright %COPYRIGHT%</em><br />
-<em>» Last changed: %CHANGED% </em><em>» Last generated: %GENERATED%</em><br />
-<em>This page has been automatically generated.</em>
-</div>
-</div>
-</body>
-</html>
diff --git a/docs/doc_header.html b/docs/doc_header.html
deleted file mode 100755
index e65ee75bce674656acf7468430cdda31c174e86f..0000000000000000000000000000000000000000
--- a/docs/doc_header.html
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<!-- -->
-<!-- Author: ROOT team (rootdev@pcroot.cern.ch) -->
-<!-- -->
-<!-- Date: %DATE% -->
-<!-- -->
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=%CHARSET%" />
-<title>%TITLE%</title>
-<meta name="rating" content="General" />
-<meta name="objecttype" content="Manual" />
-<meta name="keywords" content="jlab, cebaf, Hall C, SHMS, HMS" />
-<meta name="description" content="Hall C ROOT/C++ Analyzer." />
-<link rel="stylesheet" type="text/css" href="%RELDIR%ROOT.css" id="ROOTstyle" />
-<script type="text/javascript" src="%RELDIR%ROOT.js"></script>
-</head>
-<body onload="javascript:SetValuesFromCookie();"><div id="body_content">
-<div><center><img src="https://hallcweb.jlab.org/HallC-logo.png" alt="Hall C logo"/></center></div>
diff --git a/docs/makehtmldoc.C b/docs/makehtmldoc.C
deleted file mode 100644
index 4477e4efe462b4882a8f9fb9b42e610c0d1339f9..0000000000000000000000000000000000000000
--- a/docs/makehtmldoc.C
+++ /dev/null
@@ -1,25 +0,0 @@
-// Generate some autodoc pages by running
-// ../hcana makehtmldoc.C
-makehtmldoc() {
- THtml html;
- // Enable the "viewVC header" and "viewVC source" links to work
- // But will only work for hcana classes. Links will be broken for
- // THa classes.
- // Could probably go through all the THa*.html files that are created
- // and fix these links, but would need to know the podd branch we are on.
- html.SetViewCVS("https://github.com/JeffersonLab/hcana/tree/develop/");
- html.SetProductName("Hall C Analysis Code HCANA");
- html.SetSourceDir("..:../podd");
- html.SetIncludePath("..");
- html.SetHeader("doc_header.html");
- html.SetFooter("doc_footer.html");
- // Create documentation pages for all Classes, hcana and podd
- html.MakeAll();
- // Remake the index to list only hcana Classes. Since the
- // THa Class document pages were made, we can still click through to
- // the THa classes
- html.MakeIndex("THc");
-}
-//
-// To install, do
-// rsync -a -e ssh htmldoc/ jlabl1:/group/hallc/www/hallcweb/html/hcanadoc/