I've been using fossil for several years now, so when I set up a new fossil
my first operation is to copy over an existing .fossil-settings and commit,
so I haven't been exposed to this problem for a while.  I certainly
remember when I first used it that it did some unexpected things. Perhaps
if there is no ignore-glob or --ignore fossil should give an error pointing
out that it will put *ALL* files into the repo. (When I say error here, and
in the earlier comment) I meant a prompt that you can override (like a
cr/lf file).)

I just did the following:
------------
: /tmp ; fossil new foo.fossil
project-id: 4718320ad8895a1e5b2878f7d88ebb6b349c3777
server-id:  bf202e7dcd2d960fc5a4ead57fcd3b0ce6edb3d1
admin-user: dmason (initial password is "8bd847")
: /tmp ; cd foo
: /tmp/foo ; fossil open ../foo.fossil
project-name: <unnamed>
repository:   /private/tmp/foo/../foo.fossil
local-root:   /private/tmp/foo/
config-db:    /Users/dmason/.fossil
project-code: 4718320ad8895a1e5b2878f7d88ebb6b349c3777
checkout:     7ea66bcf3c7871acfb653662f743aa8b027d0dcc 2017-04-11 21:30:40
UTC
tags:         trunk
comment:      initial empty check-in (user: dmason)
check-ins:    1
: /tmp/foo ; echo 'int main(){}' >foo.c
: /tmp/foo ; make foo.o
cc    -c -o foo.o foo.c
: /tmp/foo ; make foo
cc   foo.o   -o foo
: /tmp/foo ; fs addremove
ADDED  foo
ADDED  foo.c
ADDED  foo.o
added 3 files, deleted 0 files
: /tmp/foo ; fossil ci -m new
./foo contains binary data. Use --no-warnings or the "binary-glob" setting
to disable this warning.
Commit anyhow (a=all/y/N)?

I would have it similarly tell you that you haven't set up "ignore-glob"
and that it will add everything and let you commit anyway, maybe with a
list of all the files it is committing. To make it go away, all you'd have
to do is ``touch .fossil-settings/ignore-blob``.

../Dave
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