This is really easy.
What format is your 2000 line CIDR list? Is it just a simple list delimited by a '\n'? Is it a Junos config? Is it Junos set commands?
If it's a list of CIDRs delimited by '\n' then use this shell script on the route engine:
admin@EX4500> start shell
% sh
$ while read cidr
do
echo "set policy-statement prefix-list test $cidr"
done
Now paste in the 2000 CIDRs and press CTRL-d after you pasted them in. This script will output the Junos commands to build a large prefix-list.
If your 2000 lines is actual Junos config, use the load command.
{master:0}[edit]
admin@EX4500# edit policy-options
{master:0}[edit policy-options]
admin@EX4500# load merge terminal relative
[Type ^D at a new line to end input]
If you have 2000 lines of actual Junos set commands, just simply paste them into the router while you're in config mode.
The fastest method is to SCP the Junos code snippet into your home directory and just use the load command with the file option.
admin@EX4500> configure
Entering configuration mode
The configuration has been changed but not committed
{master:0}[edit]
admin@EX4500# edit policy-options
{master:0}[edit policy-options]
admin@EX4500# load merge relative ?
Possible completions:
<filename> Filename (URL, local, remote, or floppy)
terminal Use login terminal
{master:0}[edit policy-options]
admin@EX4500# load merge relative