Fix README image paths and dot description

Fixed paths to images for new repository dotfile delineation. Added
quick readme blurb explaining differece of normal and dotfile
directories.
Readme still explained old bare-repository directory structure. Rewrote
sentences to conform to new structure.

Removed underscore from bootstrap directory, since the repository does
not organize itself through underscore prefixes anymore.
Fixed package gathering git-hook to respect new bootstrap directory.

.githooks/prepare-commit-msg

@@ -3,8 +3,9 @@
 COMMIT_MSG_FILE="$1"
 COMMIT_SOURCE="$2"
 
-pkgfileloc="$(git rev-parse --show-toplevel)/_bootstrap/packages.txt"
-pkgignoreloc="$(git rev-parse --show-toplevel)/_bootstrap/packages_ignore.txt"
+BOOTSTRAPDIR="bootstrap"
+pkgfileloc="$(git rev-parse --show-toplevel)/$BOOTSTRAPDIR/packages.txt"
+pkgignoreloc="$(git rev-parse --show-toplevel)/$BOOTSTRAPDIR/packages_ignore.txt"
 listgen="yay"
 
 err() {

README.md

@@ -13,7 +13,7 @@
 * [x] quick directory jumping using z, with fzf integration
 * [x] fzf integrations for bibtex citation, vim buffer management, most recently used switching, shell command history, and more
 
-![Overview](_assets/gaps.png)
+![Overview](.assets/gaps.png)
 
 ## Quick-Start
 
@@ -56,10 +56,13 @@ Enjoy!
 
 * Generally, most configuration for applications attempts to follow the XDG specifications, keeping configuration in .config directory and supplementary files in .local/share directory. Over time, I am moving more applications to this standard: it keeps the home directory clean, and the separation of configuration, binaries, and data relatively clear.
 * `.config/shell` contains all the general zsh/bash/sh configuration and environment variables usually contained in `.zshrc`, `.zprofile` and similar. It is divided in login shell config (loginrc.d), general shell config (rc.d) and zsh specific (zsh.d). Over time this should be migrated to specific `stow` 'units', but for now here is where it is.
-* `.config/rofi` contains additional scripts and a simple theming framework for rofi and should probably be migrated into the correct directories at some point.
-* `.local/bin` in `scripts` `stow` unit contains most executable user scripts.
+* The `zsh` directory contains all setup for the z-shell, my daily work environment. It should not be required for working with any other module but will add additional functionality to many (such as command auto-completion and so on). `sh` sets some base functionality for any shell you may wish to work in. It is, for now, the only module that is required for some other modules to work.[^shreq]
+* `rofi` contains additional scripts and a simple theming framework for rofi and should probably be reorganized to put the correct files into the correct directories (per xdg) at some point.
+* `.local/bin` in `scripts` `stow` unit contains most executable user scripts. Most of these have been migrated to their corresponding modules (e.g. if a script exclusively targets git functionality, it will live there), some stand-alone scripts remain however.
 * `.local/share/pandoc` contains configuration for academic latex (pandoc, really) writing and is of interest if you want to use this functionality.
 * `.xinitrc` is used for x initialization and program startup.
-* `.gitlab-ci.yml` is only used for simple CI code linting and static analysis on gitlab, can be deleted on individual deployments.
+* Generally, directories starting with a . are only meaningful for the *repository* not for the functionality of the machine that these dotfiles are deployed on. That means `.gitlab-ci.yml`, `.assets/`, `.stowrc` and similar files and directories will not show up in the final deployment in any home directory. Perhaps they should be called dotdot-files since they're the dotfiles for my dotfiles. 🙂 (Also, 'dotfiles'.)
 
-![Gapless](_assets/gapless.png)
+[^shreq]: I may remove this requirement in the future to make modules more self-contained. However, relying on some base utility scripts makes it easier to avoid duplicating such functionality for each individual script in other modules.
+
+![Gapless](.assets/gapless.png)