Abandoning Tinderbox and wikis; sticking with plain text

On Note-taking, wikis and Tinderbox

General lessons:

  • Wikis are bad: they will be broken if u move something. So, never use them: history is the best teacher; hyperlinks are stupid for keeping information for a long time
  • Future proof plain text (markdown) files are the best.
  • Keep all the text notes in the same folder, inside Dropbox
  • plain files can be access them by different apps (as the need arises).
  • Use services such as Simplenote and Dropbox to access them via the cloud (syncing)

    these were the steps i used to sync my notes to various apps

  • Create the notes in nvALT
  • Store them in a folder in Dropbox
  • Index the folder in Devonthink
  • Sync nvALT to Simplenote
  • Sync Tinderbox to Simplenote
  • Sync Scrivener to Simplenote

    Work on any of the app, as the need arises. The changes will be reflected everywhere (windows pcs, ipad, iphone, all fetch from the same folder).

  • nvALT is the best for simple notes (drop what is in your head)
  • Tinderbox is best for creating connections of ideas
  • Scrivener is the best for drafting

After some more experiences and lessons, I realize that the syncing between Simplenote and Tinderbox is broken. Tinderbox adds some weird symbols to my text when I sync them to it via Simplenote. I have been waiting for Tinderbox six if it can solve the problem. It turns out that Tinderbox 6 is by no means better than the previous version in this regard. Its arcane nature, its little communication with other applications in Mac still remains a major issue.

Therefore, I am forced to abandon it for now< at least until the formatting problem is solved. (I requested Mark Bernstein, the developer of Tinderbox a number of times, to fix the issue. Even if he promised so many times, I haven’t seen him doing it for over a year now. so, I am losing hope with him too)

Abandoning Tinderbox also invalidates Simplenote’s fuction. so, I am also not using simplenote anymore.

The whole writing system is build around dropbox now (the nvALT) folder. For creating connections between ideas, now, I have to rely on Scrivener and Devonthink (and Scapple for visualization).

now, more simplified steps:

  • Create the notes in nvALT
  • Store them in a folder in Dropbox
  • Index the folder in Devonthink
  • Sync nvALT folder to Scrivener via Folder sync

Simpler and more efficient, at least until i need visualization of my notes (which happens rarely)..

Scientific research workflow, mac

I am now starting up my PhD in linguistics. I have already collected more 1500 PDF articles and books (also did my MA in linguistics). So, I am trying to build up as perfect  workflow as possible  for my future research works. The university has given me a macbook pro, so , I am no more using windows OS. Even if there doesn´t seem to exist any comparable application in Mac as MS OneNote, I am discovering quite powerful apps in mac OS too. I have already learned a lot about Devonthink, Cirus Punies Notebook, Curio, Tinderbox and the like great apps. Therefore, I will be recording my experiences with each of the apps I am trying until I come up with the final, perfect system for my work flow.   I will write a detailed review of each of the applications here in the future. But, for now , I will just put only a short summary of my experiences with them.

1. File Organizer

My first task is to properly setup files organized in a specific folder, to make them easily accessible via Spotlight (or Alfred, I prefer the latter though). For file, organization, I use two tools; Dropbox folder and Mendeley. Dropbox doesn´t require explanation. I use mendeley not only to collect references, but also rename and organize my PDFs. It is such a powerful application to do these tasks. Here I use it.

a-I set a folder in Finder, I call it “agglomeration”, to mean, a folder where I drop all newly downloaded PDFs. All the PDF I download from internet directly go there. I use a download manager  called folx to force all the pdf files to go to this folder.  You can google it.

b-I have another folder in Dropbox, call it “AllLing”. This is the folder where I keep properly organized files.

c. Then, I setup Mendeley to suck-in all the PDFs available in the  “agglomeration” folder into its library, rename and then put them all into  “AllLing” folder.

As you can see from the above screenshot, the Mendeley is organizing my PDFs into a folder, inside Dropbox. Since the files will be renamed to Author-year-title, I can search the files using any of these attributes.  I also index the folder “AllLing” into Devonthink (see next). One main reason I want to use Mendeley is the fact that it live syns Bibtex files , even if it is not as elegant as I wish it to be. Other reference managers such as Sente and Papers are great by their own, but are weaker in their integration with bibtex.

2.Database manager:

Database managers are tools to  organize files and information in a manageable manner.  I use Devonthink this purpose.  Devonthink is one of the most powerful apps I have ever seen in the  mac environment. It has an artificial intelligence which looks inside the PDF files and establish content-based relation among the PDFs. That means, if I am reading an article on “Definiteness” , the software can scan its database, find and suggest relevant articles,  articles that contain the word “definiteness” or/and other  related words in the articles for me. It is also packed with many other interesting features such as  tagging system,   notes-taking tool; organize files into different folders, smart folders, duplicate detection, replication (aliases) etc. If you are staring to use the app, the learning could be a bit steep. I definitely recommend you to watch a screen cast in  a  website (it is under a paywall unfortunately) called screencastonline. Their screencast gave me a good ground on  Devonthink. (Note: I don´t have any affiliation with any of the links I mention here). Devonthink will be an    indispensable part of  to my workflow. I have tried some of the other database apps. I think no other app as good as Devonthink for managing scientific papers. Therefore, my database agenda is closed. The challenge I am facing is to make other applications to work with Devonthink.

So, Mendeley renames and puts the files in “AllLing”; Devonthink indexes them. I then group, replicate, organize, tag the files in the Devonthink so that I could organize them for my specific projects. I am right now writing a paper about Nominalization. Hence, I search and “see also” the related papers in Devonthink, Group them in one folder; I then drag them to Sente for reading and taking notes.

3. PDF annotation and note-taking:

Macadamec has already written a great post about Sent. I recommend visiting his  post; I am not going to repeat the whole story here. I will just shortly reflect my own experience with the application and its place in my work flow.

I  am considering totally leaving Mendeley and migrating to Sente because of the fact that the application has a more elegant tools of annotating PDFs. It can directly quite, snapshot, highlight and insert all these into the Notes panel. That is brilliant. It can also rename files, just like Mendeley. The notes then could be exported to Devonthink or Scrivener using some apple scripts. brilliant!

Sente  has some fundamental flaws, unfortunately, that makes me nervous to totally migrate my data from Mendeley:

a. it fails to import PDFs from other applications,

b. the link between the note and the pdf could also be broken. Some people have experienced this problem, and I had the same issue with a few PDF annotations.  Right now, I am using it only as PDF annotation, not as a reference manager. My references and PDFs remain in Mendeley while I temporarily import the PDFs I want to read into Sente.  (just search in Alfred and drag it to Sente because the files are properly renamed by Mendeley, or go to the folder “Allling” and drag the file; but, I usually drag them from Devonthink).

c. it is also bad for Latex integration

d. Annotations are not stored in the PDF: this the problem of almost all the note-taking tools in Mac; they store the annotations in their own database. If you open a PDF from Dropbox in another PDF reader or browser, you couldn´t see the annotation done in Sente (or Mendeley or Papers) while the annotation done in Acrobat or Foxit or PDFexchange are there, everywhere you have the pdf. Storing the annotation is good for long term use, as these applications could break. But, Sente couldn´t do it, unfortunately.


Here, the choice is clear. Since all the notes are exported from Sente in either OPML or RTFD format, I just import them to Scrivener.

5. Final Polishing and Publishing:

I export my draft form Scrivener in Latex format, I import the text to TexStudio, a latex editor that I use to finally polish my work. Texstudio, and also TexShop, can automatically detect and insert my references  which are stored in Jabref (in sync with Mendeley).

Finally, a shinny PDF!


Must have windows 7 applications

Here, I will list some of the best windows application that, I presume, that every windows user “need” to have. Of course, there are a dozen of tech magazines and website that list a dozen of such stuffs. These sources can tell you all the powers that the applications can do, the features they come with. But, the writers of thee sources rarely tell you the actual experience they have with the applications. Yes, some many application these come crammed with so many great features. These so many features, however,  usually obscure the main objectives that the applications made for. That is what makes a pedantic application different from a usable application. Usability is what most tools lack these days. They cause you more confusion and annoyance than enjoyment and service.  Here, I will mention some of applications that I found to be more useful, based on my experience. Let me start from the academic tools

Academic Apps

LaTex (freeware) for writing your documents. If you have some serous academic paper to write, you have to get LaTex. But, for simple texts, stick with Microsoft Windows  or whatever text processing apps you have.

Notepad++(freeware) for text editing; TextStudio for LaTex documents; emacs/vim if you are a serous programmer.

Jabref: to manage your bibliography, if you are using Latex.

Mendeley Desktop to organize your PDF files: Currently there is no any alternative than mendeley to manage your pdf files. it is a great too. it can extract the metadata of the files, tag from Google Scholar, and even rename  and organize your files into groups.

PDF-Exchange to read PDF: you can also try Foxit. These two softwares are equally efficient for reading PDF files, though the former has more features in the free version than the latter.

Microsoft OneNote: for more serous notes. yes, Evernote is one of the greatest tools for clipping pages from websites and writing your own notes. But, after some practice and learning a lot about these two applications, I found OneNote to be better than Evernote, specially to write more serous notes. The way OneNote organizes the notes more intuitive and robust than Evernote. Now, it can also synchronize your note online (with SkyDrive).

Dropbox for your cloud computing needs. You already know it!

Calibre: to manage your ebooks. If you have e-reader like Nook or Kindle, the chances are you have a dozen of ebooks (EPub or Mobi) files. Calibre can help you to clean up the clutter. It can also convert from one format to the other. The best in the game!

Wordweb: desktop dictionary. No doubt, Wordweb is the most popular and the best dictionary application for windows. Lingoes is also great.

CutePDF: to convert your documents into PDF

Adobe Pro: to convert PDF files to other formats such as word, excel etc

Media Apps

MediaMonkey:for audio. MM is the best and probably the only software you need  to manage your music and audiobook. I know so many people use iTunes.  The main turn off for me with iTunes is the fact that it stores metadata about my files in a separate folder. That means, if you edit (tag) the name of the singer, the Album, the CD cover, all these information will be stored in iTunes library, not with your actual files. If you want to migrate to another application some time, you will lose all the editing you did on your files. You will not get the name of the artist, not the album…. That is bad. I want my files as clean and edited as I want. MediaMonkey can do it and store the information with the files. MediaMonkey also has better editing (tagging) tools than iTunes.

The KMPlayer: for videos. I know many people prefer VLC player. VLC is great for the fact that it can play almost all links of video/audio files you throw in to it. But, I found The KMPlayer more efficient in managing my video file. It can also play  all the popular video files.

Other Utilities

Google Chrome for browsing: I am sure you have already tried Chrome. it is a great  browser. It also seems a bit faster than Firefox.

UTorrent: small but efficient torrent downloader. you have to download the earlier version of uTorrent (2.1 or earlier)  if you what small size and efficient torrent downloader. The new versions have been damn shit!

IDM: for downloading files from internet: Internet download manager is  the fastest download manager in the market.  There are some other free alternatives to it. But, yah. I am not as such satisfied with them.

Revo Uninstaller: to uninstall applications. it removes all the junkie that uninstalled applications leave behind.

Ditto: to manage your clipboards. It keeps the contents you copied for latter use.

Everything: for desktop searching. Windows has its own desktop search engine. But, Everyting does the job faster. Switching off the search indexing of  the windows also helps your computer to perform  faster.

Directory Opus. Though  quite expensive, Opus is the best desktop explorer software. It has been two years since I used the regular explorer.

Avast free: for antivirus. Both avast and avira are great  antivirus programs. I prefer avast for two reasons. First, it doesn’t display adds ( Avira had been quite intrusive for some time. I am not sure right now if it still displays adds so aggressively as before). Secondly, it uses less resources than avira (in my pc)

Evernote: to clip webpages from website and write down notes.

7zip: to extract archive files: a free, fast  and powerful software! You get almost all the features of the expensive extractors such as winrar. Just wonderful!

Bulk Rename Utility: for renaming files, though its interface is ugly,  there is not better software than this one! It does the job very well

Tell me your favorite application!

Organize audio-books in iPod (iPhone) using MediaMonkey, the best method so far!

I LOVE audio-books. I enjoy listening them and learn a lot faster with them than reading. I usually listen  them in my leisure times, while doing some  physical exercise as in the gym, in the bus, while walking my ass …Winking smile. They are just great tools of learning; and  the iPhone (iPod) is a brilliant devise for audios. I also have Oxford & American Heritage dictionaries in it  to check out new words.  I know no other phone that has a better an application to manage audiobooks as well as great dictionary as Oxford and American Heritage. The main reason I bought the iPhone is of course for the audio-books.   

In this shallow world where substantive things lose value and triviality has got the utmost attention though, music has received more emphasis over audiobooks. Hence, Mr. Apple doesn’t take the case of audiobooks seriously in its devices. iPod is the perfect tool for music but not really as great as one expects for audio-books. There are a few tricks that you can do to get the books into the iPod; but not as such satisfactory specially when it comes to organization. I have tried different methods to organize my audio-books, to get each of the files in the books in a proper order so that listening would be more joy, organized and deductive. But, my frustration with ITunes was limitless. Spending hours and hours to make my audio-books easily accessible for  listening, I was not able to get all as I wanted. I have tried renaming the files, putting them into playlists, tagging track numbers etc. with no success.  The following two problems where specially annoying me all the time.

1. ITunes doesn’t allow importing many CDs of the same book as a single book.  If you want to get your audiobooks into your iPhone, you have to store them as music Albums. That is the trick you need to learn if you want to manage your books in iTunes.  But, storing audiobooks as music albums couldn’t give  you the flexibility to store different sections/chapters of the books as chapters/sections. I used to listen to an English vocabulary book called Verbal Advantage, as I mentioned before. The book has 24 CDS. I have to store each of the CDS as   separate books in the iPhone. This makes the ipod a total mess. While I had only about 90 audiobooks, the iPod actually used to display more than 300 audiobooks. That is just uncomfortable to browse the books. I want all the CDs as a single book. iTunes has a small trick thing to join the files of the CDs; I have used it for some time. But, that doesn’t work with mp3.

2. It Messes up track numbers: this is the terrible problem. In the middle of the listening, the the narration jumps from track 03 to 40. I have tried different methods to solve the problem in iTunes. Just terrible problems reappear now and then. 

I then discovered  MediaMonkey. It is not discovery actually. I have been using the software to manage music for about three years now. I can dare to say, MM is by far the best media  management software; and its tagging feature is  so incredible. I love it in all my heart. But, I was not able to get it work with my iPhone for some reason. Finally, I learned that the problem was related with QuickTime. Though there is not explicit requirement about the QuickTime, I found my iPhone failing to synchronize without it. So, I installed it beside iTunes. Everything works fine now. So, in this page, I will show you how you can exploit the powers of  MM to manage your audiobooks.

So, here is how I get the  best result in MM: 4 simple steps

1. Rename the files properly
2. Import them into MM
3. Tag the Title of the files from the file names
4. Remove the Track#
5. Voila!

1. The first step is  to properly rename your audio files. The renaming is necessary because tagging can be done from the name of the files. I use a software called Bulk Rename Utility to rename my files; an ugly, but so powerful software! it makes the renaming so simple. 

Just add some meaningful numbers as prefixes in the files, as

CD1-01 Introduction

CD1-02 ….



In this picture for example, I am simply prefixing CD7  on the existing names. The presix makes the iPod to arrange the files accordingly. The Bulk Renaming Utility (the book is “Verbal Advantage” as can you can see on the left side in the picture) can do complicated naming. You can add just prefixes, as I did here, Find and Replace, add numbers as Prefixes, etc.  This way of renaming, I will give your files a consistent file name that could  order them even if they are in the same folder. The file name also will function as the Title for the audio-files (as I will show you next). After prefixing the CD-numbers in each of the files,  I may then put all the files of the 24 disks into one folder(if I want to). Then

2. Import them into MM. I assume you know how the basics of MM. Go to Files->Add/Rescan files –>choose the folder where you have your audiobook; “[test]-Verbal Advantage” in my case. MM will import all the files in the folder.

3. Tag the files using the “auto-tag from file name” feature of MediaMonkey. Before you do the tagging, you have to select all the imported files of the book in MM. I selected all the files in the 24 CDs of the Verbal Advantage. You then go to Tools menu in MM and click on “auto-tag from file name”.  You will get a dialog box. In there, you will see the power of MM. It gives you the choices to tag Albums, Tracks, Artists etc from the file name. You can  specify to tag two or more features at the same time. But, for now, tagging the Titles of the audios from the filenames is quite sufficient. So, choose only <title> from the box and remove the others. MM will mark blue on the files that their Title is going to change.

Here is the screen- shot of the tagging window.  


The one I marked with red, for example, shows that the old Title “Introduction” is going to be replaced by a new title “CD-01-Introduction”. Click ok

4. Remove the Track# from the files. This is what motivated me to write this page today. Renaming and importing the files as I have described so far used to give me quite inconsistent results. For a reason I couldn’t explain, I sometimes used to get messed up orders of files in my iPhone. This morning, I discovered that the culprit is the Track# that the files come with. So, I have to remove it before I import the files into my iPhone. To do so, select all the files as usual –> right click –>properties . You will get a window. This is where you can insert the full metadata about your audiobook in MM. Here is what you have to do if you are not familiar with MM’s audiobook (music) management system.

a)  File path—leave it blank

b)  File Name—blank again

c)  Title –blank

d) Type: “audiobook” <—this is very important. your iPod will recognize the audiobook as  music otherwise. If you are using the older version of MM, you need to mark “audiobook” in the “Genre(s)” field.

e) Artist—write the artist(author) : “Charles Harrington Elster” in my case

f)  Track#: leave the box black, but tick the box in front of it. This will remove all the old track numbers stored in the files.


Note that deleting the track number is necessary only if you find it offending. If the the track numbers are properly set, they are great assets actually. So, the first thing is to try to synchronize the files to your iPhone and see of the order is good enough. If you find some files misplaced, say the 12th set as 2nd in the order, you need to go and remove the track number of those files (or from all the files). If you find the whole CDx (or a chunk of files) misplaced, probably, the Disk# is the culprit. So, go and remove (fix) it.

But, I have found one special advantage in removing track# totally from my files.  If the track#s are removed, the Titles (filenames) of the files  will be clearly visible in my iPod; otherwise, the iPod will be showing me only the track numbers (as 3 of 20). Being able to read the titles is actually good idea b/c you will be able to read in which chapter, section or subsection you are in, how the sections/chapters are organized enhancing your  comprehension; you can also easily skip the  chapter/topic that you are not interest in ; or just jump forth to the sections of your special interest. When I was listening  Bertrand Russel’s classic, “The History of Western Philosophy”, I had been skipping some of the sections about certain specific philosophers such as Hume and Descartes because I already heard (read) enough about them, targeting on less known ones helps me to get new ideas. The following picture is snapped from MM’s window. The names and numbers under Title column (marked Blue) will be visible in my iPhone. If I had no the Track# removed and hence  the Titles invisible in my iPod, I wouldn’t be able to see which section is about which philosopher, hence, forced to listen every section.


(You can, by the way, use an application called FlickTunes to supplement your Title reading experience in your iPod app. Search it in App Store.)

5. Transfer the files into your iPhone. Now, you have perfectly ordered files in your iPhone (iPod) stored as a single book. You don’t need to worry about jumping back and forth in the book; no clutter in your iPod; no hassling with playlists…. just play the first piece and enjoy your book to the end in one move!

Open-mouthed smileDelluOpen-mouthed smile

Organize audiobook in ipod (iphone) in Mediamonkey, best result

I LOVE audio-books. I enjoy listening them and learn a lot faster with them than reading. I listen them while doing some other physical work; as in the gym…they are just great tools of learning; and  an the iphone (ipode) is the best devise for audio. I know no other phone that has an application to manage audiobooks.  In this shallow world where substantive things lose value, music has got more emphasis over audiobooks. Hence, the Apple doesn’t take the case of audiobooks seriously in its devices. Ipod is good for music but not for audio-books. There is not good way of managing audio-books.

I have tried different methods to organize my audio-books. My frustration with Itunes was limitless. Spending hours and hours to make my audio-books easily accessible for easy listening had been so pain. The main problems were:

  1. Itunes doesn’t allow importing many CDs of the same book. If you want to get your audiobooks into your iphone, you have to store them as Albums. Storing audiobooks as music albums doesn’t give  me the flexibility to store different sections/chapters of the books as chapters/sections. I used to listen to an English vocabulary book called Verbal Advantage, as I mentioned before. The book has 24 CDS. I have to store each of the CDS as   separate books in the iphone. This makes the iphone a total clutter.
  2. it Messed up track numbers: this is the terrible problem. In the middle of the listening, the the voice jumps from track 03 to 40. I have tried playlists, renaming the files, properly tagging them. All didn’t work. just terrible problems reappear now and then.

I then shifted to MediaMonkey. I can dare to say, MM is the best media management software; and its tagging feature is  so incredible. But, you have to make sure that you installed itunes and  Quicktime for MM to work. Though there is not explicit requirement about the latter, I found my iphone failing to synchronize without it.

So, here is how I get the  best result in mediamonkey.

  1. First, you have to properly rename your audio files. The renaming is necessary because tagging can be done from the name of the files. I use a software called Bulk Rename Utility to rename my files; an ugly, but so powerful software! it makes the renaming so simple.

Here is how you can rename your files

CD1-01 Introduction

CD1-02 ….


In this picture for example, I am simply adding a prefix (CDx) in the Bulk Renaming Utility. This way, you will give your files a consistent file name that could  order them even if they are in the same folder. Then

  1. Import them into MM. I assume you know how the basics of MM.

  2. Tagg the files using the “auto-tag from file name” feature in mediamonkey. Before you do the tagging, you have to select all the imported files of the book in MM. You then go to Tools menu in MM and click on “auto-tag from file name”.  You will get a dialog box. In there, you have to specify what you are going to tag. Tagging the Titles of the audios from the filenames is quite sufficient. So, choose only <title> from the box. Let me, for example, show you how I tagged a 3CD book called  “Letting go of God” by Julia Sweeney. (don’t forget, I have renamed the files into CD1-01, CD1-02 etc. then, i have imported them; and selected all the files in the MM, then I am tagging them from the file names). So, here is the screen shot of the tagging process.

Reading inside Mendeley, better to avoid it

I have already started writing about the great research tool, Mendeley Desktop. I believe, mendeley is one of the mandatory tools every academician need to have. Many people are using it for many things. As to me, however, its main virtue is the ability to organize the actual PDF files in a brilliant manner. In this post, though, I am going to tell you why you need to avoid reading and annotating PDF files inside Mendeley itself.

If you are familiar with the fast and efficient PDF readers as Foxit and PDF-exchange, you will face too many constraints with Mendeley’s internal PDF reader, which I found to be unbearable. Of course, you can read, annotate and write notes inside mendeley. But, the main downside of Mendeley’s internal PDF reader is the fact that your annotations will be saved in separate folder. Mendeley has a system called database where it saves information about the PDF files. That database is in a different folder from the actual PDF files. Hence, if you open your Mendeley annotated PDF files in another PDF reader, you will not get the annotations. This is bad. I want my PDFs annotated wherever I open them, whenever I want.

Mendeley team has tried to alleviate the problem by adding a feature to export the annotations of the PDFs. But, I found this to be a laborious task. Should I open and export the annotations of each and every file every time I want to see my annotations in another software? no, I will not do it. So, if you are like me, the best approach is to manage your files inside Mendeley and read them using more potent PDf readers as Foxit. Your annotations and notes will be saved embedded inside the PDF files that you don’t have to worry opening them in another software.  You will enjoy your annotations to the  end of time (unless you want to remove them of course) wherever you go, which ever software you use.  So, to  open the files organized inside Mendeley with external readers, you have to right clicking the file and choose “Open file externally”. Your default reader will be fired. Voila!


Converting PDF to Epub (Mobi) format, the best method/result so far

I have tried a dozen of methods to convert my PDF books to EPub format; Most of the time, the result is frustrating. Numbering, page setup, footnotes, headers, pictures  all get messy in the result.

But, now, for the first time, after a desperate digging,  I am getting satisfactory results. That is the good new. I am going to tell you how to do it.

First, the necessary tools (The first three are the most popular ones in the ebook world.) with their strengths and weakness in short.

1. Calibere is the best tool to manage books. But, the conversion is so bad. So, use it to manage and view your ebooks. But, avoid converting pdf in it.

2. Mobipocket Creater. This is good for converting html to prc. PRC format can be opened in Kindle (app). But, it can not convert to epub format.

3. Sigil: this is wonderful tool to edit and convert texts (including html) to epub. it can not import PDF.

Finally, the most powerful software to convert PDFs into Epub, though few people ever know its function for ebook conversion;

4. ABBYY Finereader 11. This is the most effective tool I have ever tried to convert PDF (picture) files to other formats (texts such as html, word etc). The result is so shinning.  The new version (v. 11)   also natively supports conversion to Epub.

So, the first thing to do is to import your PDF file to ABBYY Finereader11. You will get every kind of text format out of it including html and epub.  You can spell-check it, edit the font, page setup. Almost everything that Sigil can do. The best of all,  ABBYY can remove headers and footnotes (this had been a pain in my ass when I was using Adobe pro to convert PDF to html).  The only weakness of the ABBYY Finereader is on the Table of Contents. It can not generate Toc  in the epub format. So, to solve this problem (to get Toc in my epub), I use the following two methods.

Two best ways to generate the Table of Contents

A. (recommended)  Convert the Pdf to html in Abby FineReader and then edit the html in Sigil by marking Headings; generate the TOc from the heads, and finally to Epub. Since this method gives the most accurate result for the Toc, one can implement it  in when one needs a detailed/best Toc; when when when the pdf doesn’t contain bookmarks. But this method could be  time consuming to mark every section and subsection as a Heading in Sigil.

B. Bookmark the Chapters (sections) of the PDF  before importing it to ABBYY in any pdf reader (foxit/adobe). The booksmarks then can  serve as Toc after cenversion in ABBYY. If you want to use the bookmakrs of the file as Toc, direct converstion to epub in ABBYY  cuts away sub-sections (only the main chapters, beginning from 2nd chapter appear in the epub). May be because of a little bug, only the main chapters/sections of the PDF beggining from Chapter/section 2 appear in the epub result. Therefore, if you want to get  all the detailed bookmarks of the PDF as contents in the epub, it is necessary to avoid direct converstion to Epub in ABBYY. Rather, convert the PDF   to html  (the bookmarks of the PDF come out as hyperlinks in the html) and then  import the html either into Sigil or Mobipocket Creater. In Sigil, directly converting the html to Epub gives the bookmarks keeps the hiperlinks of in the epub (The hyperlink can serve as Toc by choosing “go to start” in the Epub readers such as  Nook and  Kindle). To use the hyperliks of the html as Toc in Mobipocket Creater, you need to edit the html file in a text editor following  this  guide. Note that the result is of the Mobipocket Creater is prc. You can read the prc in Kindle, or futher convert it to epub.

->Mobi format can easily be generated from the epub, using Calibere.