dvc add a file from data directory

[dmpetrov]

From a discussion with users: https://opendatascience.slack.com/archives/CGGLZJ119/p1579704007005600 (you need access to this community)

$ mkdir datadir
$ cp ~/whatever/* datadir/
$ dvc add datadir/
WARNING: Output 'datadir' of 'datadir.dvc' changed because it is 'modified'
To track the changes with git, run:

          git add datadir.dvc
$ cp ~/Downloads/newfile.csv datadir/jan2020.csv
$ dvc add datadir/jan2020.csv
ERROR: Paths for outs:                  # <-- error is terrible btw (not related to this issue).
'datadir'('datadir.dvc')
'datadir/file4'('datadir/file4.dvc')
overlap. To avoid unpredictable behaviour, rerun command with non overlapping outs paths.

The last command fails because the file is inside a data dir and you suppose to update (dvc add) the entire dir. However, a user intuition says (for some users) to add a single file.

Ideally, this should work:

$ dvc add datadir/jan2020.csv
'jan2020' was added to dir 'datadir' and 'datadir.dvc' changed because it is 'modified'
100% Add|██████████████████████████████████|1.00/1.00 [00:00<00:00,  2.76file/s]

To track the changes with git, run:

	git add datadir.dvc

[efiop]

I'm not sure about this implicit behavior. A user might not even notice that we did that trick and be then surprised that his file doesn't have their own dvc file. This is the only case where we've seen a report like that, so I would rather wait for someone else to report it, to understand if this is a one-off cofusion of particular user or something reoccurring.

[efiop]

From conversation with @dmpetrov it is clear that he has seen other occurences of this issue and it would be great to at least improve the error

[pared]

Reproduction script:

#!/bin/bash

rm -rf repo

mkdir repo

set -ex

pushd repo

git init --quiet && dvc init -q

mkdir data
echo 1 >> data/1

dvc add data

echo 2 >> data/2

dvc add data/2

[pared]

@efiop @dmpetrov I created pull request that suggests user how this situation should be handled,
do you want to continue work, and make dvc autocommit new file?