[FIX] Broken scaffold no more

[SamGuay]

• When dcm2bids_scaffold was ran multiple times, it appended data inside the generated files multiple times instead of overwriting it when using --force.
• The URL for the README was the the raw README, so HTML was being parsed, fixed that as well.
• There was no logging, so I added some, including a tree representation of the output_dir in which the scaffold was done. No additional dependency was added.
• Create a .bidsignore which include tmp_dcm2bids that is not valid, partially answering a comment brought up in Move tmp directory #195

[codecov-commenter]

Codecov Report

Merging #209 (62d5e44) into master (86f89e3) will increase coverage by 0.50%.
The diff coverage is 90.69%.

@@            Coverage Diff             @@
##           master     #209      +/-   ##
==========================================
+ Coverage   80.07%   80.57%   +0.50%     
==========================================
  Files          15       15              
  Lines         833      865      +32     
  Branches      137      143       +6     
==========================================
+ Hits          667      697      +30     
- Misses        134      136       +2     
  Partials       32       32              

Flag	Coverage Δ
pytest	80.57% <90.69%> (+0.50%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
dcm2bids/cli/dcm2bids_scaffold.py	89.74% <90.00%> (+2.24%)	⬆️
dcm2bids/utils/utils.py	82.75% <90.62%> (+3.44%)	⬆️
dcm2bids/utils/io.py	72.00% <100.00%> (-3.87%)	⬇️

... and 1 file with indirect coverage changes

[arnaudbore]

LGTM - fix pep8 and it's GTG