atlas overwrites user files

[timotheecour]

Example

cd $dir
git clone https://github.com/nim-lang/Nim
cd Nim
sh build_all.sh
ls ..
Nim
bin/nim c -r tools/atlas/atlas.nim clone https://github.com/disruptek/balls
ls ..

Current Output

it generates directories outside of source tree

Nim             balls           grok            nim-bytes2human npeg            packages        sync            testes          ups

and in fact in my use case that prompted this issue, it affected and modified existing files I had in Nim/.. as that directory already contained some cloned packages.

Expected Output

it should generate directories self-contained within source tree:

Nim

possibly under: Nim/.atlas, similar to node_modules/

rationale: things should be kept self contained, so you won't interfere with other local installations of nim (i have more than 1 nim folder for development purposes, branches don't solve everything).

Additional Information

1.5.1 98f7254

see also #18751

[Araq]

Works as documented.