OK, turns out Gergely's suggestion to use rm -rf subDirectory works, and 
removes the directory and all its files. The GitBash pointer has to be on 
the directory that contains the subDirectory. I was earlier trying it while 
pointing to the subDirectory, and it fails there. After removing all the 
subdirectories, the directory headers were left over. I moved the pointer 
up a directory, cd ..  and used rmdir --ignore-fail-on-non-empty newProject 
to remove the last of this mess.

My overall commentary on this saga is: 
1. Git has a major failing because it can contain directories and files 
that do not show in Windows7, even when Show Hidden Files is enabled. I 
have struggled for 2 weeks because the problem files are not visible in 
Windows, yet git says not empty and won't clone into the target directory. 
This should be a high priority for Git developers to fix.
2.git help turns out to be useful, but other documentation, tutorials, and 
the ProGit book are inadequate because: A. they are not clear about the 
differing impacts of a command on a directory, vs a file, vs a repository, 
vs whatever these imaginary things were that I have been working (these 
imaginary things not showing in Windows are not even mentioned in git 
sources) ,  B. they do not describe how to extract yourself from major 
problems. The descriptions are all "business as usual". Some of them are 
complex, but they are business as usual, and C. they don't describe how to 
start up in an Apache web server htdocs directory. Its an obvious place to 
have files that need version control.
3.The community is the valuable resource. I especially thank Nelson and 
Gergely for their clues that headed me in the right direction. Their advice 
was more useful than entire chapters of ProGit.

On Monday, March 24, 2014 2:17:35 PM UTC-4, Michael Laird wrote:
> I want to clone a directory of files to start my first AngularJS project 
> and put those files in Apache's htdocs directory with the name of my 
> project, e.g., newProject. I've used the ProGit book, a bunch of tutorials, 
> and Stackoverflow, and after many hours, still don't have it.
> From all my first attempt messing around, I may have 'polluted' my git. 
> With no newProject directory in the htdocs directory (ie, after deleting 
> prior copies), I point git at htdocs and get a command prompt ending in 
> htdocs. There, I can do a cd newProjects and get a new command prompt 
> ending in htdocs/newProject, even though the directory does not exist. A 
> git status returns fatal:not a git repo (or any of parent directories): 
> .git I have tried rm -rf .git at that prompt and get no git response, just 
> another same commmand prompt. What's going on? I have recently deleted git, 
> and re-installed a new download, so maybe this is no longer an issue.
> When I add a newProject directory to htdocs and do what ProGit says
> git clone git://github.com/angular/angular-seed.git newProject
> I get fatal:destination path newProject exists and is not empty, even 
> though Windows Explorer says it is an empty directory, and a git status at 
> that prompt says fatal:not a repo (. . .) .git
> When I try the commands at How do you clone a git repository into a 
> specific 
> folder?<http://stackoverflow.com/questions/651038/how-do-you-clone-a-git-repository-into-a-specific-folder>as
>  follows
> git clone git://github.com/angular/angular-seed:newProject htdocs
> I get fatal:destination path newProject exists and is not empty A git 
> status at that prompt returns fatal: not a repository 
> I have also tried the above command without the htdocs, and get the same 
> result.
> Now that I have re-installed a new download of git, I need to do a correct 
> command to clone the angular-seed directory of files and get it renamed 
> newProject in a directory several levels down in Windows7, called 
> apache2/htdos. What do I do?

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