1. Install Ghostscript  (PostScript and PDF language interpreter and pre‐viewer), use command:

# sudo apt-get install gs

2. Install PDFtk (A handy tool for manipulating PDF), using command:

# sudo apt-get install pdftk

3. run the command line

Merge 2 files (or more) into one file:
pdftk doc_1.pdf doc_2.pdf doc_3.pdf cat output doc_combined_123.pdf

Other Commands:

Using Handles:
pdftk A=doc_1.pdf B=doc_2.pdf cat A B output doc_combined_12.pdf

Using Wildcards:
pdftk *.pdf cat output doc_combined.pdf

Split Selected Pages from Multiple PDFs into one new PDF file:
pdftk A=one.pdf B=two.pdf cat A1-7 B1-5 A8 output combined.pdf

Encrypt a PDF using default 128-Bit Strength and Withhold All Permissions:
pdftk mydoc.pdf output encrypted_doc.128.pdf owner_pw your_password_here

Same as Above, Except a Password is Required to Open the PDF:
pdftk mydoc.pdf output encrypted_doc.128.pdf owner_pw blablabla user_pw helloworld

Same as Above, Except Printing is Allowed (after the PDF is Open):
pdftk mydoc.pdf output encrypted_doc.128.pdf owner_pw blablabla user_pw helloworld allow printing

Decrypt:
pdftk encrypted_doc.pdf input_pw helloworld output decrypted_doc.pdf