Toward the less-addressed organizational aspect of the question, I find that I need to maintain a fairly structured organization in order to effectively manage my papers, presentation, code, etc. over time. My methods result in a minor amount of duplication, but it is rare and there are never more than 3 copies of a document at the very most. This is, of course, my own idiosyncratic system, but perhaps it will be useful as inspiration or a template for how you think about developing your own.
First, my driving principles of organization:
- Since collaborative projects have to be shared in so many different ways, I do not use any specialty organizational software, but just the hierarchy of the file system.
- My primary sorting heuristic mirrors how I organize my time (and how it is attributed to projects in funding bookkeeping)
- Higher level directory names are shorter, since they are more persistent and more frequently typed; lower level names are as long as they need to be to understand what they are far in the future.
- No directory should have more than a dozen or so subdirectories
Following these principles, my first layer of directories are sorted by the main business functions of academia:
- pursuit: all proposals and funding pursuit goes here
- projects: this directory contains one subdirectory for each funded project that is currently active (plus one for each major line of preliminary work). Rationale: each grant/contract needs to have its activities tracked individually for reporting to the funder.
- internal: administrative dealings with my institution, such as travel receipts, training documents, and internal process documents go here. Travel receipts get their own subdirectory.
- service: professional service, including teaching, recommendation letters, conference organization, seminar series, journal editing, and reviewing. One subdirectory for each major topic (e.g., one for each conference, another for all recommendation letters).
- notes: all personal notes and reading, with a subdirectory for talk notes, another for manuals, and another for downloaded papers (with further subdirectories for major topics)
- sites: contains one directory for each website where I am one of the maintainers.
Every one of these also contains either an archive subdirectory, where I move completed tasks, either by topic (e.g., pursuit, projects) or by year (e.g., internal, service).
In any second-level directory, I maintain a README file that tells me what I will need to know when I re-visit something after forgetting all about it. The directories for funded projects also have a stereotyped structure:
- contract: This is where all contract documents go for funded projects.
- admin: all reporting, deliverables, etc.
- publications: each paper gets its own directory; the conference presentation for a paper and any derivative papers also go here.
- presentations: all presentations not directly associated with a paper go here
- Beyond that, there are directories for each major strand of work in the project
- For publications, every published paper (and supplement) also gets a copy, with a long informative name including the year, in the publications directory for my professional website.
- For collaborative projects, there may also be a top-level split between internal and shared, with certain documents having a master version in internal and a second copy in shared.
Finally, everything that I care about must be backed up in two different ways:
- By the backup system of each machine that I use.
- By means of some sort of synchronization software (with version control when possible). I am currently using a mixture of SVN, git, Mercurial, Dropbox, and BitTorrent Sync, chosen per-project based on the collaborators.