use Fcntl;

...

my $flags |= O_NONBLOCK;
fcntl($JSWRITE, F_SETFL, $flags);

...
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Your program works fine for me when I run a Perl script for the child.

my $pid = open2($JSREAD, $JSWRITE, q{perl -e"{ $_=<>; last if /^END$/;
+ ++$i; $m=qq{$i: $_}; warn $m; print $m; redo}"});
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(The $|=1 isn't even necessary!)

Seems to me the problem is in the js side. But I doubt it's in readline. Are you sure your Perl script reaches END? Are you sure END is causing the child to exit?

By the way, you're adding newlines where they already exist in two different places.

Yes, you're right about the unnecessary newlines. I fixed the newline where it feeds the file one line at a time to the child. The perl absolutely reaches "END".

test.js is three simple lines:

var foo=0;
var bar=1;
var baz=2;
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And I can type these in, one at a time, into the running javascript program from the command line:

$ js
js> load('jslint.js');
var foo=0;
var bar=1;
var baz=3;
END
jslint: No problems found.

$
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If I drop warns in:

open FILE, '<', "test.js";
while (<FILE>)
{
    warn "printing $_";
    print $JSWRITE "$_";
}
close(FILE);

warn "printing END\n";
print $JSWRITE "END\n";
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I see:

$ ./jslint.pl 
printing var foo=0;
printing var bar=1;
printing var baz=3;
printing END
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And strace shows this:

...
write(4, "load(\'jslint.js\');\n", 19)  = 19
open("test.js", O_RDONLY)               = 3
ioctl(3, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff8d5e9440) = -1 ENOTTY (I
+nappropriate ioctl for device)
lseek(3, 0, SEEK_CUR)                   = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=33, ...}) = 0
fcntl(3, F_SETFD, FD_CLOEXEC)           = 0
read(3, "var foo=0;\nvar bar=1;\nvar baz=3;"..., 4096) = 33
write(2, "printing var foo=0;\n", 20printing var foo=0;
)   = 20
write(4, "var foo=0;\n", 11)            = 11
write(2, "printing var bar=1;\n", 20printing var bar=1;
)   = 20
write(4, "var bar=1;\n", 11)            = 11
write(2, "printing var baz=3;\n", 20printing var baz=3;
)   = 20
write(4, "var baz=3;\n", 11)            = 11
read(3, "", 4096)                       = 0
close(3)                                = 0
write(2, "printing END\n", 13printing END
)          = 13
write(4, "END\n", 4)                    = 4
close(4)                                = 0
read(5,  <unfinished ...>
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Which, if I remove reading from $JSREAD, becomes:

write(4, "load(\'jslint.js\');\n", 19)  = 19
open("test.js", O_RDONLY)               = 3
ioctl(3, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff38afb950) = -1 ENOTTY (I
+nappropriate ioctl for device)
lseek(3, 0, SEEK_CUR)                   = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=33, ...}) = 0
fcntl(3, F_SETFD, FD_CLOEXEC)           = 0
read(3, "var foo=0;\nvar bar=1;\nvar baz=3;"..., 4096) = 33
write(2, "printing var foo=0;\n", 20printing var foo=0;
)   = 20
write(4, "var foo=0;\n", 11)            = 11
write(2, "printing var bar=1;\n", 20printing var bar=1;
)   = 20
write(4, "var bar=1;\n", 11)            = 11
write(2, "printing var baz=3;\n", 20printing var baz=3;
)   = 20
write(4, "var baz=3;\n", 11)            = 11
read(3, "", 4096)                       = 0
close(3)                                = 0
write(2, "printing END\n", 13printing END
)          = 13
write(4, "END\n", 4)                    = 4
close(4)                                = 0
close(5)                                = 0
wait4(8790,  <unfinished ...>
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