Some uses of Phan may involve passing it a list of files instead of using .phan/config.php

You can pass the files to be analyzed to Phan on the command-line, but with a large code base, you'll want to create a file that lists all files and filters out junk to make your life easier.

One way to generate this file list would be to create a file .phan/bin/mkfilelist (like Phan's) with the following contents.

#!/bin/bash
if [[ -z $WORKSPACE ]]
then
    export WORKSPACE=~/path/to/code/src
fi
cd $WORKSPACE
JUNK=/var/tmp/junk.txt
for dir in \
    src \
    vendor/path/to/project
do
    if [ -d "$dir" ]; then
        find $dir -name '*.php' >> $JUNK
    fi
done
cat $JUNK | \
    grep -v "junk_file.php" | \
    grep -v "junk/directory.php" | \
    awk '!x[$0]++'
rm $JUNK

You can then run ./.phan/bin/mkfilelist > files. Take a look at Phan's file list generator to see an example.

With this, you can now run phan -f files to run an analysis of your code base. (If .phan/config.php exists in the working directory, phan -f files will use configuration settings from that file, but the files from that list)