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So I made the mistake of making everything 777 on my local machine. I then zipped everything, uploaded the file via FTP to my server, then used SSH to unzip it. Now everything is 777, which is obviously bad.

I figured I could do something like chmod 644 * -R, then 666 and 777 on the things that needed it. However doing 644 gives me permission denied (755 works, but I assume that is not very safe either, or?)

What should the file permissions of all files (except the 666/777 ones) be? And is there a fast way of setting them?

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You can make batch file for this - ee_permissions.sh

#!/bin/bash

# Find location of this script.
# This ensures that only files in the directory in
# which this script exists (recursively) are modified.
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

# Set what the name of your expressionengine folders are.
SYSTEM="system"
IMAGES_DIR="public_html/images"
UPLOADS_DIR="public_html/files"

# Optionally ensure correct ownership on per environment basis.
#if [ "$DIR" = "/path/to/project/" ]; then
#   chown -R http.http "$DIR"
#fi

# Expressionengine specific permissions.
find "$DIR" -type d -print0 | xargs -0 chmod 0755
find "$DIR" -type f -print0 | xargs -0 chmod 0644
find "$DIR/$IMAGES_DIR/" -type d -print0 | xargs -0 chmod -R go+w
find "$DIR/$UPLOADS_DIR/" -type d -print0 | xargs -0 chmod -R go+w
chmod -R go+w "$DIR/templates"
chmod -R go+w "$DIR/$SYSTEM/expressionengine/cache"
chmod 0666 "$DIR/$SYSTEM/expressionengine/config/config.php"
chmod 0666 "$DIR/$SYSTEM/expressionengine/config/database.php"

# Permissions specific to the sitemap generator
# from http://www.xml-sitemaps.com/.
#chmod -R 0777 "$DIR/public_html/generator/data"
#chmod 0666 "$DIR/public_html/sitemap.xml"
#chmod 0666 "$DIR/public_html/ror.xml"

# If laxative is being used, preserve executability
if [ -e "$DIR/.db/lax" ]; then
    chmod 0700 "$DIR/.db/lax"
fi

# Make sure other shell scripts are executable too.
find "$DIR" -type f -name "*.sh" -print0 | xargs -0 chmod 700

another example of shell_script for the same.

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