diff --git a/COSMOS.md b/doc/COSMOS.md
similarity index 100%
rename from COSMOS.md
rename to doc/COSMOS.md
diff --git a/doc/bibliography.md b/doc/bibliography.md
new file mode 100644
index 0000000..70e1579
--- /dev/null
+++ b/doc/bibliography.md
@@ -0,0 +1,25 @@
+# How the bibliography is made
+
+References are stored in a bibtex file. The XML file contains
+citations that are similar to a LaTeX citation command.
+
+During processing, the bibtex file and the bibliography and citation
+type (anthology or monograph, numeric or author/year) are read out of
+the XML source file.
+
+`pandoc-citeproc` is used to construct a JSON file out of the bibtex
+database. This is helpful during the next parts of processing.
+
+<!--
+ !-- What exactly is it used for? Just for putting the title in the popover element?
+  -->
+
+The next step formats the bibliography, depending on the bibliography
+type, as a complete list or as per-chapter-list. In the second case,
+several markdown and html files are created, one for each chapter.
+They are named after the `xml:id` of the chapter.
+
+The function `format_citations` then creates two outputs: the list of
+references, formatted in html and a dictionary with the citekey as
+headword and three manifestations of the data (author-year-citation,
+year-citation and title).
diff --git a/doc/create_tmpbib.md b/doc/create_tmpbib.md
new file mode 100644
index 0000000..8c15ae6
--- /dev/null
+++ b/doc/create_tmpbib.md
@@ -0,0 +1,19 @@
+# Create temporary bibliography
+
+In cases where authors hand in a formatted version of the bibliography
+(rather than a reference database), this tool can help creating a
+database in BibTeX format.
+
+Required argument is a textfile with a formatted bibliography (one
+entry per line). The option `k` is there to supply an entry with a
+keyword, for example the name of the chapter author.
+
+We require authors to use shortcuts in their docx manuscript when
+citing, including the use of a citekey (`LASTNAME_YEAR`), there should
+already be citekeys in the manuscript. When running `fix_tei.py`,
+these citekeys are gathered together and can be used as an input to
+this tool.
+
+The tool creates temporary citekeys out of the formatted bibliography
+and in an interactive session, the user selects the most likely entry.
+With this, rudimentary entries can be created.
diff --git a/doc/datapickle.md b/doc/datapickle.md
new file mode 100644
index 0000000..04299d3
--- /dev/null
+++ b/doc/datapickle.md
@@ -0,0 +1,582 @@
+# Documentation for the contents of `data.pickle`
+
+This file is quite important.
+
+What does it contain?
+
+It assigns numbers to elements. The thirteenth figure in the first (numbered) chapter
+
+It tells me that an element with a certain ID has a human readable reference
+
+    data["chapterdict"] = chapterdict
+    data["figdict"] = figdict
+    data["eqdict"] = eqdict
+    data["fndict"] = fndict
+    data["listdict"] = listdict
+    data["pagelabeldict"] = pagelabeldict
+    data["secdict"] = secdict
+    data["tabdict"] = tabdict
+    data["theoremdict"] = theoremdict
+
+
+{
+  'chapterdict':
+    {'uid1': '1',
+     'uid18': '2',
+     'uid33': '3',
+     'uid67': '4'
+     'uid114': '5',
+     'uid223': '6',
+     'uid257': '7',
+     'uid304': '8',},
+
+ 'eqdict': {},
+
+   'figdict':
+   {
+  'uid3': '1.1',
+  'uid4': '1.2',
+  'uid6': '1.3',
+  'uid7': '1.4',
+  'uid9': '1.5'
+  'uid10': '1.6',
+  'uid11': '1.7',
+  'uid12': '1.8',
+  'uid13': '1.9',
+  'uid14': '1.10',
+  'uid15': '1.11',
+  'uid16': '1.12',
+  'uid17': '1.13',
+},
+
+ 'fndict': {},
+
+ 'listdict': {
+  'uid100': '31',
+  'uid101': '32',
+  'uid102': '33',
+  'uid103': '34',
+  'uid104': '35',
+  'uid105': '36',
+  'uid106': '37',
+  'uid107': '38',
+  'uid116': '1',
+  'uid117': '2',
+  'uid118': '3',
+  'uid119': '4',
+  'uid120': '5',
+  'uid121': '6',
+  'uid122': '1',
+  'uid123': '2',
+  'uid124': '3',
+  'uid125': '4',
+  'uid126': '5',
+  'uid127': '6',
+  'uid128': '7',
+  'uid129': '8',
+  'uid130': '9',
+  'uid131': '10',
+  'uid132': '11',
+  'uid133': '12',
+  'uid134': '13',
+  'uid135': '14',
+  'uid136': '15',
+  'uid137': '16',
+  'uid138': '17',
+  'uid139': '18',
+  'uid140': '19',
+  'uid141': '20',
+  'uid142': '21',
+  'uid143': '22',
+  'uid144': '23',
+  'uid145': '24',
+  'uid146': '25',
+  'uid147': '26',
+  'uid148': '27',
+  'uid149': '28',
+  'uid150': '29',
+  'uid151': '30',
+  'uid152': '1',
+  'uid153': '2',
+  'uid154': '3',
+  'uid155': '4',
+  'uid156': '5',
+  'uid157': '1',
+  'uid158': '2',
+  'uid159': '3',
+  'uid160': '4',
+  'uid161': '5',
+  'uid162': '6',
+  'uid163': '7',
+  'uid164': '8',
+  'uid165': '9',
+  'uid166': '10',
+  'uid167': '11',
+  'uid168': '12',
+  'uid169': '1',
+  'uid170': '2',
+  'uid171': '3',
+  'uid172': '4',
+  'uid173': '5',
+  'uid174': '6',
+  'uid175': '7',
+  'uid176': '8',
+  'uid177': '9',
+  'uid178': '10',
+  'uid179': '11',
+  'uid180': '12',
+  'uid181': '13',
+  'uid182': '14',
+  'uid183': '15',
+  'uid184': '16',
+  'uid185': '17',
+  'uid186': '18',
+  'uid187': '19',
+  'uid188': '20',
+  'uid189': '21',
+  'uid190': '22',
+  'uid191': '23',
+  'uid192': '24',
+  'uid193': '25',
+  'uid194': '26',
+  'uid195': '27',
+  'uid196': '1',
+  'uid197': '2',
+  'uid198': '1',
+  'uid199': '2',
+  'uid200': '3',
+  'uid201': '4',
+  'uid202': '5',
+  'uid203': '6',
+  'uid204': '7',
+  'uid205': '1',
+  'uid206': '2',
+  'uid207': '3',
+  'uid208': '4',
+  'uid209': '5',
+  'uid210': '6',
+  'uid211': '7',
+  'uid212': '8',
+  'uid213': '9',
+  'uid214': '1',
+  'uid215': '2',
+  'uid216': '3',
+  'uid217': '4',
+  'uid218': '5',
+  'uid219': '6',
+  'uid220': '1',
+  'uid221': '2',
+  'uid224': '1',
+  'uid225': '2',
+  'uid226': '3',
+  'uid227': '4',
+  'uid228': '5',
+  'uid229': '6',
+  'uid230': '7',
+  'uid231': '8',
+  'uid232': '9',
+  'uid233': '10',
+  'uid234': '11',
+  'uid235': '12',
+  'uid236': '13',
+  'uid237': '14',
+  'uid238': '15',
+  'uid239': '16',
+  'uid240': '17',
+  'uid241': '18',
+  'uid242': '1',
+  'uid243': '2',
+  'uid244': '3',
+  'uid245': '4',
+  'uid246': '5',
+  'uid247': '6',
+  'uid248': '7',
+  'uid249': '8',
+  'uid250': '9',
+  'uid251': '10',
+  'uid252': '11',
+  'uid253': '12',
+  'uid254': '13',
+  'uid255': '14',
+  'uid256': '15',
+  'uid260': '1',
+  'uid261': '2',
+  'uid262': '3',
+  'uid263': '4',
+  'uid264': '5',
+  'uid265': '6',
+  'uid266': '7',
+  'uid267': '8',
+  'uid268': '9',
+  'uid269': '10',
+  'uid270': '11',
+  'uid271': '12',
+  'uid272': '13',
+  'uid273': '14',
+  'uid274': '15',
+  'uid275': '16',
+  'uid276': '17',
+  'uid277': '18',
+  'uid278': '19',
+  'uid279': '20',
+  'uid280': '21',
+  'uid281': '22',
+  'uid282': '23',
+  'uid283': '24',
+  'uid284': '25',
+  'uid285': '26',
+  'uid286': '27',
+  'uid287': '28',
+  'uid288': '29',
+  'uid289': '30',
+  'uid290': '31',
+  'uid291': '32',
+  'uid292': '33',
+  'uid293': '34',
+  'uid294': '35',
+  'uid295': '36',
+  'uid296': '37',
+  'uid297': '38',
+  'uid306': '1',
+  'uid307': '2',
+  'uid308': '3',
+  'uid309': '4',
+  'uid310': '5',
+  'uid311': '6',
+  'uid312': '1',
+  'uid313': '2',
+  'uid314': '3',
+  'uid315': '4',
+  'uid316': '5',
+  'uid317': '6',
+  'uid318': '7',
+  'uid319': '8',
+  'uid320': '9',
+  'uid321': '10',
+  'uid322': '11',
+  'uid323': '12',
+  'uid324': '13',
+  'uid325': '14',
+  'uid326': '15',
+  'uid327': '16',
+  'uid328': '17',
+  'uid329': '18',
+  'uid330': '19',
+  'uid331': '20',
+  'uid332': '21',
+  'uid333': '22',
+  'uid334': '23',
+  'uid335': '24',
+  'uid336': '25',
+  'uid337': '26',
+  'uid338': '27',
+  'uid339': '28',
+  'uid34': '1',
+  'uid340': '29',
+  'uid341': '30',
+  'uid342': '1',
+  'uid343': '2',
+  'uid344': '3',
+  'uid345': '4',
+  'uid346': '5',
+  'uid347': '1',
+  'uid348': '2',
+  'uid349': '3',
+  'uid35': '2',
+  'uid350': '4',
+  'uid351': '5',
+  'uid352': '6',
+  'uid353': '7',
+  'uid354': '8',
+  'uid355': '9',
+  'uid356': '10',
+  'uid357': '11',
+  'uid358': '12',
+  'uid359': '1',
+  'uid36': '3',
+  'uid360': '2',
+  'uid361': '3',
+  'uid362': '4',
+  'uid363': '5',
+  'uid364': '6',
+  'uid365': '7',
+  'uid366': '8',
+  'uid367': '9',
+  'uid368': '10',
+  'uid369': '11',
+  'uid37': '4',
+  'uid370': '12',
+  'uid371': '13',
+  'uid372': '14',
+  'uid373': '15',
+  'uid374': '16',
+  'uid375': '17',
+  'uid376': '18',
+  'uid377': '19',
+  'uid378': '20',
+  'uid379': '21',
+  'uid38': '5',
+  'uid380': '22',
+  'uid381': '23',
+  'uid382': '24',
+  'uid383': '25',
+  'uid384': '26',
+  'uid385': '27',
+  'uid386': '1',
+  'uid387': '2',
+  'uid388': '3',
+  'uid389': '4',
+  'uid39': '6',
+  'uid390': '5',
+  'uid391': '6',
+  'uid392': '7',
+  'uid393': '1',
+  'uid394': '2',
+  'uid395': '3',
+  'uid396': '4',
+  'uid397': '5',
+  'uid398': '6',
+  'uid399': '7',
+  'uid40': '7',
+  'uid400': '8',
+  'uid401': '9',
+  'uid402': '1',
+  'uid403': '2',
+  'uid404': '3',
+  'uid405': '4',
+  'uid406': '5',
+  'uid407': '6',
+  'uid408': '1',
+  'uid409': '2',
+  'uid41': '8',
+  'uid42': '9',
+  'uid43': '10',
+  'uid44': '11',
+  'uid45': '12',
+  'uid46': '13',
+  'uid47': '14',
+  'uid48': '15',
+  'uid49': '16',
+  'uid50': '17',
+  'uid51': '18',
+  'uid52': '1',
+  'uid53': '2',
+  'uid54': '3',
+  'uid55': '4',
+  'uid56': '5',
+  'uid57': '6',
+  'uid58': '7',
+  'uid59': '8',
+  'uid60': '9',
+  'uid61': '10',
+  'uid62': '11',
+  'uid63': '12',
+  'uid64': '13',
+  'uid65': '14',
+  'uid66': '15',
+  'uid70': '1',
+  'uid71': '2',
+  'uid72': '3',
+  'uid73': '4',
+  'uid74': '5',
+  'uid75': '6',
+  'uid76': '7',
+  'uid77': '8',
+  'uid78': '9',
+  'uid79': '10',
+  'uid80': '11',
+  'uid81': '12',
+  'uid82': '13',
+  'uid83': '14',
+  'uid84': '15',
+  'uid85': '16',
+  'uid86': '17',
+  'uid87': '18',
+  'uid88': '19',
+  'uid89': '20',
+  'uid90': '21',
+  'uid91': '22',
+  'uid92': '23',
+  'uid93': '24',
+  'uid94': '25',
+  'uid95': '26',
+  'uid96': '27',
+  'uid97': '28',
+  'uid98': '29',
+  'uid99': '30'},
+
+ 'pagelabeldict': {
+     'img001': ' on input line 3',
+     'img002': ' on input line 4',
+     'img003': ' on input line 5',
+     'img004': ' on input line 6',
+     'img005': ' on input line 7',
+     'img006': ' on input line 8',
+     'img007': ' on input line 9',
+     'img008': ' on input line 10',
+     'img009': ' on input line 11',
+     'img010': ' on input line 12',
+     'img011': ' on input line 13',
+     'img012': ' on input line 14',
+     'img013': ' on input line 15',
+     'img014': ' on input line 16',
+     'img015': ' on input line 17',
+     'img016': ' on input line 18',
+     'img017': ' on input line 19',
+     'img018': ' on input line 20',
+     'img019': ' on input line 21',
+     'img020': ' on input line 22',
+     'img021': ' on input line 23',
+     'img022': ' on input line 24',
+     'img023': ' on input line 25',
+     'img024': ' on input line 26',
+     'img025': ' on input line 27',
+     'img026': ' on input line 28',
+     'img027': ' on input line 29',
+     'img028': ' on input line 30',
+     'img029': ' on input line 31',
+     'img030': ' on input line 32',
+     'img031': ' on input line 33',
+     'img032': ' on input line 34',
+     'img033': ' on input line 35',
+     'img034': ' on input line 36',
+     'img035': ' on input line 37',
+     'img036': ' on input line 38',
+     'img037': ' on input line 39',
+     'img038': ' on input line 40',
+     'img039': ' on input line 41',
+     'img040': ' on input line 42',
+     'img041': ' on input line 43',
+     'img042': ' on input line 44',
+     'img043': ' on input line 45',
+     'img044': ' on input line 46',
+     'img045': ' on input line 47',
+     'img046': ' on input line 48',
+     'img047': ' on input line 49',
+     'img048': ' on input line 50',
+     'img049': ' on input line 51',
+     'img050': ' on input line 52',
+     'img051': ' on input line 53',
+     'img052': ' on input line 54',
+     'img053': ' on input line 55',
+     'img054': ' on input line 56',
+     'img055': ' on input line 57',
+     'img056': ' on input line 58',
+     'img057': ' on input line 59',
+     'img058': ' on input line 60',
+     'img059': ' on input line 61',
+     'img060': ' on input line 62',
+     'img061': ' on input line 63',
+     'img062': ' on input line 64',
+     'img063': ' on input line 65',
+     'img064': ' on input line 66',
+     'img065': ' on input line 67',
+     'img066': ' on input line 68',
+     'img067': ' on input line 69',
+     'img068': ' on input line 70',
+     'img069': ' on input line 71',
+     'img070': ' on input line 72',
+     'img071': ' on input line 73',
+     'img072': ' on input line 74',
+     'img073': ' on input line 75',
+     'img074': ' on input line 76',
+     'img075': ' on input line 77',
+     'img076': ' on input line 78',
+     'img077': ' on input line 79',
+     'img078': ' on input line 80',
+     'img079': ' on input line 81',
+     'img080': ' on input line 82',
+     'img081': ' on input line 83',
+     'img082': ' on input line 84',
+     'img083': ' on input line 85',
+     'img084': ' on input line 86',
+     'img085': ' on input line 87',
+     'img086': ' on input line 88',
+     'img087': ' on input line 89',
+     'img088': ' on input line 90',
+     'img089': ' on input line 91',
+     'img090': ' on input line 92',
+     'img091': ' on input line 93',
+     'img092': ' on input line 94',
+     'img093': ' on input line 95',
+     'img094': ' on input line 96',
+     'img095': ' on input line 97',
+     'img096': ' on input line 98',
+     'img097': ' on input line 99',
+     'img098': ' on input line 100',
+     'img099': ' on input line 101',
+     'img100': ' on input line 102',
+     'img101': ' on input line 103',
+     'img102': ' on input line 104',
+     'img103': ' on input line 105',
+     'img104': ' on input line 106',
+     'img105': ' on input line 107',
+     'img106': ' on input line 108',
+     'img107': ' on input line 109',
+     'img108': ' on input line 110',
+     'img109': ' on input line 111',
+     'img110': ' on input line 112',
+     'img111': ' on input line 113',
+     'img112': ' on input line 114',
+     'img113': ' on input line 115',
+     'img114': ' on input line 116',
+     'img115': ' on input line 117',
+     'img116': ' on input line 118',
+     'img117': ' on input line 119',
+     'img118': ' on input line 120',
+     'img119': ' on input line 121',
+     'sec10:Figure10': '41',
+     'sec11:Figure11': '43',
+     'sec12:Figure12': '45',
+     'sec13:Figure13': '47',
+     'sec1:Figure1': '11',
+     'sec2:Figure2': '13',
+     'sec3:Figure3': '17',
+     'sec4:Figure4': '26',
+     'sec5:Figure5': '31',
+     'sec6:Figure6': '32',
+     'sec7:Figure7': '33',
+     'sec8:Figure8': '35',
+     'sec9:Figure9': '37'
+     },
+ 'secdict': {
+     'uid2': '1.1',
+     'uid5': '1.2',
+     'uid8': '1.3',
+     'uid19': '2.1',
+     'uid20': '2.2',
+     'uid21': '2.2.1',
+     'uid22': '2.2.2',
+     'uid23': '2.2.3',
+     'uid24': '2.2.4',
+     'uid25': '2.2.5',
+     'uid26': '2.3',
+     'uid27': '2.3.1',
+     'uid28': '2.3.2',
+     'uid29': '2.3.3',
+     'uid30': '2.3.4',
+     'uid31': '2.3.5',
+     'uid32': '2.3.6',
+     'uid68': '4.1',
+     'uid69': '4.2',
+     'uid108': '4.3',
+     'uid109': '4.4',
+     'uid110': '4.5',
+     'uid111': '4.6',
+     'uid112': '4.7',
+     'uid113': '4.8',
+     'uid115': '5.1',
+     'uid222': '5.2',
+     'uid258': '7.1',
+     'uid259': '7.2',
+     'uid298': '7.3',
+     'uid299': '7.4',
+     'uid300': '7.5',
+     'uid301': '7.6',
+     'uid302': '7.7',
+     'uid303': '7.8',
+     'uid305': '8.1',
+     'uid410': '8.2',
+     },
+ 'tabdict': {},
+ 'theoremdict': {}}
diff --git a/doc/eoaclassic-workflow.md b/doc/eoaclassic-workflow.md
new file mode 100644
index 0000000..8ebb561
--- /dev/null
+++ b/doc/eoaclassic-workflow.md
@@ -0,0 +1,35 @@
+# The EOA classic workflow
+This document documents the different parts of the *EOA classic* workflow, which is based on EOATeX files.
+
+## eoatex2imxml.py
+### Steps in this program
+- Preparation, setup and checks
+- Tralics conversion of EOATeX source
+  - Includes slight output correction
+- Processing elements
+  - Mostly chapter by chapter
+- Creation of bibliographical entries
+- Cleanup
+- Write output files and data
+### Available functions
+- getchildren
+- TeX2PNG
+- makebibchecker
+- sanitizebibentry
+- createBibEntryAuthorYear
+- createBibEntryNumeric
+- pdf_burst
+- progress
+- cleanup
+## imxml2django.py
+## imxml2epub.py
+## imxml2tei.py
+## Libraries
+### libeoabibitem.py
+### libeoaconvert.py
+## Other files
+### config
+### debug
+### mkimage.py
+### data
+### tmp_files
diff --git a/doc/eoadocx-workflow.md b/doc/eoadocx-workflow.md
new file mode 100644
index 0000000..24d7728
--- /dev/null
+++ b/doc/eoadocx-workflow.md
@@ -0,0 +1,6 @@
+# The EOA DocX workflow
+This document documents the different parts of the *EOA TEI* workflow, which is based on DocX files.
+
+
+tei2eoatex.xsl
+tei2imxml.py
diff --git a/metadatamapping.md b/doc/metadatamapping.md
similarity index 100%
rename from metadatamapping.md
rename to doc/metadatamapping.md