clay: mounted desk retains files deleted on unix if there's a commit error on the first try

[tinnus-napbus]

Describe the bug

If you |merge %foobar our %base, delete all the files in it on unix, copy your own files across, and then |commit but the commit fails for whatever reason, then when you fix the issue and recommit the files you deleted won't actually be deleted. This results in people unknowingly distributing the entire %base desk along with their app. It's particularly an issue if they're distributing a desk without their own desk.bill file, eg they're just distributing a glob webapp or whatever, cos it'll have the base desk desk.bill file and consequently start copies of all the base desk agents, which will shut down the actual base desk ones and transfer their state across.

To Reproduce
Steps to reproduce the behaviour:

1. |merge %foobar our %base
2. cd ~/piers/zod/foobar
3. rm -r * .
4. cp ~/your-desk/* .
5. |commit %foobar
6. (failure cos you missed a mark file dependency or whatever)
7. you fix the issue
8. you rerun |commit %foobar
9. all the files you deleted are not deleted on %foobar, so your desk actually includes the whole %base desk, which you probably didn't notice unless you were paying careful attention to the commit printout in the dojo

Expected behaviour
If you delete files on unix they should be deleted upon |commit in all cases

Screenshots

See screen recording of reproducing bug

System (please supply the following information, if relevant):

• OS: Arch linux x86-64 desktop

Additional context
This could account for why many 3rd party desks are seemingly distributing %base

Notify maintainers

@liam-fitzgerald

[tomholford]

6.(failure cos you missed a mark file dependency or whatever)

While preparing for distribution of an app, I ran into the error described above a couple times. Even though the app is just a glob of JS & HTML, it takes up a significant amount of size as reported by |mass.

Here's a comparison of several desks, note the size of %hodl:

        %fafa: 
          %ankh: KB/4.488
          %mime: KB/4.512
          %ford-files: KB/492.208
          %ford-naves: B/0
          %ford-marks: B/0
          %ford-casts: B/0
          %ford-tubes: B/0
        --KB/501.208
        %garden: 
          %ankh: KB/64.556
          %mime: KB/12.668
          %ford-files: MB/1.804.396
          %ford-naves: KB/8.400
          %ford-marks: KB/104.816
          %ford-casts: KB/1.872
          %ford-tubes: KB/4.608
        --MB/2.001.316
        %gora: 
          %ankh: KB/5.784
          %mime: KB/4.648
          %ford-files: MB/2.699.372
          %ford-naves: B/0
          %ford-marks: B/0
          %ford-casts: B/0
          %ford-tubes: B/0
        --MB/2.709.804
        %hodl: 
          %ankh: MB/146.294.204
          %mime: MB/18.496.528
          %ford-files: MB/9.325.136
          %ford-naves: KB/182.356
          %ford-marks: KB/2.496
          %ford-casts: KB/7.104
          %ford-tubes: KB/3.960
        --MB/174.311.784

[tinnus-napbus]

you should be able to tell definitively if you run +tree /=hodl=/sys or +tree /=hodl=/app or whatever and see a whole lot of files you didn't intend to include

[tomholford]

you should be able to tell definitively if you run +tree /=hodl=/sys or +tree /=hodl=/app or whatever and see a whole lot of files you didn't intend to include

Looks like %base is indeed being included:

> +tree /=hodl=/app
/app/acme/hoon
/app/aqua/hoon
/app/azimuth/hoon
/app/azimuth/logs/eth-logs
/app/azimuth/version-0/azimuth-snapshot
/app/azimuth-rpc/hoon
/app/azimuth-tracker/hoon
/app/claz/hoon
/app/dbug/hoon
/app/debug/css/index/css
/app/debug/index/html
/app/debug/js/channel/js
/app/debug/js/index/js
/app/debug/js/tile/js
/app/dns-collector/hoon
/app/dojo/hoon
/app/eth-sender/hoon
/app/eth-watcher/hoon
/app/gaze/hoon
/app/herm/hoon
/app/hood/hoon
/app/language-server/hoon
/app/lens/hoon
/app/ping/hoon
/app/roller/hoon
/app/roller-rpc/hoon
/app/shoe/hoon
/app/spider/hoon
/app/test/hoon
/app/time/hoon
> +tree /=hodl=/sys
/sys/arvo/hoon
/sys/hoon/hoon
/sys/kelvin
/sys/lull/hoon
/sys/vane/ames/hoon
/sys/vane/behn/hoon
/sys/vane/clay/hoon
/sys/vane/dill/hoon
/sys/vane/eyre/hoon
/sys/vane/gall/hoon
/sys/vane/iris/hoon
/sys/vane/jael/hoon
/sys/zuse/hoon

[tinnus-napbus]

If you run +agents %hodl, assuming you didn't delete the base desk's desk.bill file, you'll see that your desk is running all the base agents. I believe you'll need to |rein %base to stop them on %hodl and start them again on %base. This could be a problem for people who've installed your app

[tinnus-napbus]

cos your desk will have basically stolen the state of all the base agents

[ynx0]

%hodl is the new %base