How do I set up my own certificate authority

Question

I tried google on the above question, and the most recent thing I found was 7 years old. replacing the phrase used generates a lot of hits with a very poor signal to noise ratio.
I have OpenSSL (in the cygwin distribution), which is quite recent, but frankly its documentation leaves just about everything to be desired. I found pyca, but it has no documentation at all (and it is a couple years old).
I tried the steps appended below, but invariably the attempt to sign the certificates fails with an obscure error message about OpenSSL not finding one thing or another.
At this stage, I just don't care whether I do this using something in the J2SDK such as keytool or OpenSSL, as long as I can get it done. Or if there is some other opensource software tool I can use, terrific. This is primarily for the purpose of securing communications within an Intranet, and secondarily for signing applets and applications distributed through WebStart. If I am not mistaken, I'll need a certificate for each of my servers. Right?
If you know of an URL where this is well explained and illustrated, great. Give that to me.
Otherwise, a simple illustration (or a correction of what I've appended below) would be appreciated. I believe I understand what ought to be happening. It ought to be rather simple to do, but there are these irritating and frustrating minor details getting in the way. For example, the steps I show below seem simple, but everything appears to get messed up by some of the contents of openssl.cnf in 'usr/ssl', in the cygwin directory, and there is no explanation of how to set things up for the first time you use OpenSSL within Cygwin (or on unix for that matter).
Any assistance would be appreciated.
Thanks,
Ted
========failed attempt=====================
# Generation of Certificate Authority(CA)
openssl req -new -x509 -keyout cakey.pem -out cacert.pem -config /usr/ssl/openssl.cnf
# Create server request and key
openssl req -new -keyout server-key.pem -out server-req.pem -days 36502 -config /usr/ssl/openssl.cnf
# Remove the passphrase from the key
openssl rsa -in server-key.pem -out server-key.pem
# Sign server cert
openssl ca -policy policy_anything -out server-cert.pem -infiles server-req.pem -config /usr/ssl/openssl.cnf
# Create client request and key
openssl req -new -keyout client-key.pem -out client-req.pem -days 36502 -config /usr/ssl/openssl.cnf
# Remove a passphrase from the key
openssl rsa -in client-key.pem -out client-key.pem
# Sign client cert
openssl ca -policy policy_anything -out client-cert.pem -infiles client-req.pem -config /usr/ssl/openssl.cnf

Answer 1

The following works for me:
NB: Some of the output has been removed in the interests of privacy (this will not affect the outcome)
1. Create CA key and certificate
1.1 Create a new file called "serial" containing the value "01".
1.2 Create an empty file "index.txt"
1.3 Create a subdirectory "newcerts"
1.4 Execute.... create a key for your CA
[ben@localhost ca]$ openssl genrsa -out ca.key 2048
Generating RSA private key, 2048 bit long modulus
.....................................+++
..........................................................+++
e is 65537 (0x10001)
1.5 Execute... create a certificate for your own CA
[ben@localhost ca]$ openssl req -config ./openssl.cnf -new -x509 -key ca.key -out cacert.pem -days 365
You are about to be asked to enter information that will be incorporated
into your certificate request.
What you are about to enter is what is called a Distinguished Name or a DN.
There are quite a few fields but you can leave some blank
For some fields there will be a default value,
If you enter '.', the field will be left blank.
Country Name (2 letter code) [GB]:
County or State (full name) []:
City or town (eg, Hitchin) []:
Organization Name (eg, company) []:
Organizational Unit Name (eg, section) []:
Common Name (eg, your name or your server's hostname) []:
Email Address []:
2. Create PK key and .csr
2.1 Execute...
[ben@localhost ca]$ keytool -genkey -alias PK
Enter keystore password: password
What is your first and last name?
[Unknown]:
What is the name of your organizational unit?
[Unknown]:
What is the name of your organization?
[Unknown]:
What is the name of your City or Locality?
[Unknown]:
What is the name of your State or Province?
[Unknown]:
What is the two-letter country code for this unit?
[Unknown]:
Is CN=, OU=, O=, L=, ST=, C=GB correct?
[no]: yes
Enter key password for <PK>
(RETURN if same as keystore password):
2.2 Create .csr
[ben@localhost ca]$ keytool -certreq -alias PK -file PK.csr
Enter keystore password: password
3. Sign PK with CA cert
[ben@localhost ca]$ openssl ca -config ./openssl.cnf -in PK.csr -out PK.pem -keyfile ca.key -days 365
Using configuration from ./openssl.cnf
Check that the request matches the signature
Signature ok
Certificate Details:
Serial Number: 0 (0x0)
Validity
Not Before: Jan 5 19:48:33 2006 GMT
Not After : Jan 5 19:48:33 2007 GMT
Subject:
countryName = GB
stateOrProvinceName =
organizationName =
organizationalUnitName =
commonName =
X509v3 extensions:
X509v3 Basic Constraints:
CA:FALSE
Netscape Comment:
OpenSSL Generated Certificate
X509v3 Subject Key Identifier:
D6:2D:7E:71:77:9E:1A:BB:54:69:98:63:6A:6A:E2:BA:12:C4:D7:DD
X509v3 Authority Key Identifier:
keyid:92:7C:33:7C:EC:1D:76:C5:B8:F0:30:6D:10:12:40:E5:E7:EA:24:31
DirName:/C=GB/ST=/L=/O=/OU=/CN=/emailAddress=
serial:F0:D1:38:36:65:6D:71:D5
Certificate is to be certified until Jan 5 19:48:33 2007 GMT (365 days)
Sign the certificate? [y/n]:y
1 out of 1 certificate requests certified, commit? [y/n]y
Write out database with 1 new entries
Data Base Updated
4. Convert PK certificate into DER format
[ben@localhost ca]$ openssl x509 -in PK.pem -out PK.der -outform DER
5. Import CA certificate into keystores
[ben@localhost ca]$ keytool -import -alias ca -file cacert.pem
Enter keystore password: password
Owner: EMAILADDRESS=, CN=, OU=, O=, L=, ST=, C=GB
Issuer: EMAILADDRESS=, CN=, OU=, O=, L=, ST=, C=GB
Serial number: f0d13836656d71d5
Valid from: Thu Jan 05 19:41:09 GMT 2006 until: Fri Jan 05 19:41:09 GMT 2007
Certificate fingerprints:
MD5: AF:3D:8E:25:12:24:04:1F:40:70:BC:A0:9E:0E:44:84
SHA1: B8:E8:0B:A5:86:33:21:0C:B5:3C:6E:F2:DE:7B:31:0F:59:AE:21:E4
Trust this certificate? [no]: yes
Certificate was added to keystore
6. Import signed PK into keystore
[ben@localhost ca]$ keytool -import -alias pk -file PK.der
Enter keystore password: password
Certificate reply was installed in keystore
REF:
http://www.yorku.ca/dkha/docs/jsse_cert/jsse_cert.htm
http://httpd.apache.org/docs/2.2/ssl/ssl_faq.html#ownca
http://www.openssl.org/docs/apps/ca.html#
openssl.cnf:#
# OpenSSL example configuration file.
# This is mostly being used for generation of certificate requests.
# This definition stops the following lines choking if HOME isn't
# defined.
HOME               = .
RANDFILE          = $ENV::HOME/.rnd
# Extra OBJECT IDENTIFIER info:
#oid_file          = $ENV::HOME/.oid
oid_section          = new_oids
# To use this configuration file with the "-extfile" option of the
# "openssl x509" utility, name here the section containing the
# X.509v3 extensions to use:
# extensions          =
# (Alternatively, use a configuration file that has only
# X.509v3 extensions in its main [= default] section.)
[ new_oids ]
# We can add new OIDs in here for use by 'ca' and 'req'.
# Add a simple OID like this:
# testoid1=1.2.3.4
# Or use config file substitution like this:
# testoid2=${testoid1}.5.6
[ ca ]
default_ca     = CA_default          # The default ca section
[ CA_default ]
dir          = .               # Where everything is kept
certs          = $dir/certs          # Where the issued certs are kept
crl_dir          = $dir/crl          # Where the issued crl are kept
database     = $dir/index.txt     # database index file.
#unique_subject     = no               # Set to 'no' to allow creation of
                         # several ctificates with same subject.
new_certs_dir     = $dir/newcerts          # default place for new certs.
certificate     = $dir/cacert.pem      # The CA certificate
serial          = $dir/serial           # The current serial number
#crlnumber     = $dir/crlnumber     # the current crl number must be
                         # commented out to leave a V1 CRL
crl          = $dir/crl.pem           # The current CRL
private_key     = $dir/private/cakey.pem# The private key
RANDFILE     = $dir/private/.rand     # private random number file
x509_extensions     = usr_cert          # The extentions to add to the cert
# Comment out the following two lines for the "traditional"
# (and highly broken) format.
name_opt      = ca_default          # Subject Name options
cert_opt      = ca_default          # Certificate field options
# Extension copying option: use with caution.
# copy_extensions = copy
# Extensions to add to a CRL. Note: Netscape communicator chokes on V2 CRLs
# so this is commented out by default to leave a V1 CRL.
# crlnumber must also be commented out to leave a V1 CRL.
# crl_extensions     = crl_ext
default_days     = 365               # how long to certify for
default_crl_days= 30               # how long before next CRL
default_md     = md5               # which md to use.
preserve     = no               # keep passed DN ordering
# A few difference way of specifying how similar the request should look
# For type CA, the listed attributes must be the same, and the optional
# and supplied fields are just that :-)
policy          = policy_match
# For the CA policy
[ policy_match ]
countryName          = match
stateOrProvinceName     = match
organizationName     = match
organizationalUnitName     = optional
commonName          = supplied
emailAddress          = optional
# For the 'anything' policy
# At this point in time, you must list all acceptable 'object'
# types.
[ policy_anything ]
countryName          = optional
stateOrProvinceName     = optional
localityName          = optional
organizationName     = optional
organizationalUnitName     = optional
commonName          = supplied
emailAddress          = optional
[ req ]
default_bits          = 1024
default_keyfile      = privkey.pem
distinguished_name     = req_distinguished_name
attributes          = req_attributes
x509_extensions     = v3_ca     # The extentions to add to the self signed cert
# Passwords for private keys if not present they will be prompted for
# input_password = secret
# output_password = secret
# This sets a mask for permitted string types. There are several options.
# default: PrintableString, T61String, BMPString.
# pkix      : PrintableString, BMPString.
# utf8only: only UTF8Strings.
# nombstr : PrintableString, T61String (no BMPStrings or UTF8Strings).
# MASK:XXXX a literal mask value.
# WARNING: current versions of Netscape crash on BMPStrings or UTF8Strings
# so use this option with caution!
# we use PrintableString+UTF8String mask so if pure ASCII texts are used
# the resulting certificates are compatible with Netscape
string_mask = MASK:0x2002
# req_extensions = v3_req # The extensions to add to a certificate request
[ req_distinguished_name ]
countryName               = Country Name (2 letter code)
countryName_default          = GB
countryName_min               = 2
countryName_max               = 2
stateOrProvinceName          = County or State (full name)
stateOrProvinceName_default     =
localityName               = City or town (eg, Hitchin)
localityName_default          =
0.organizationName          = Organization Name (eg, company)
0.organizationName_default     =
# we can do this but it is not needed normally :-)
#1.organizationName          = Second Organization Name (eg, company)
#1.organizationName_default     = World Wide Web Pty Ltd
organizationalUnitName          = Organizational Unit Name (eg, section)
organizationalUnitName_default     =
commonName               = Common Name (eg, your name or your server\'s hostname)
commonName_max               = 64
emailAddress               = Email Address
emailAddress_max          = 64
# SET-ex3               = SET extension number 3
[ req_attributes ]
challengePassword          = A challenge password
challengePassword_min          = 4
challengePassword_max          = 20
unstructuredName          = An optional company name
[ usr_cert ]
# These extensions are added when 'ca' signs a request.
# This goes against PKIX guidelines but some CAs do it and some software
# requires this to avoid interpreting an end user certificate as a CA.
basicConstraints=CA:FALSE
# Here are some examples of the usage of nsCertType. If it is omitted
# the certificate can be used for anything *except* object signing.
# This is OK for an SSL server.
# nsCertType               = server
# For an object signing certificate this would be used.
# nsCertType = objsign
# For normal client use this is typical
# nsCertType = client, email
# and for everything including object signing:
# nsCertType = client, email, objsign
# This is typical in keyUsage for a client certificate.
# keyUsage = nonRepudiation, digitalSignature, keyEncipherment
# This will be displayed in Netscape's comment listbox.
nsComment               = "OpenSSL Generated Certificate"
# PKIX recommendations harmless if included in all certificates.
subjectKeyIdentifier=hash
authorityKeyIdentifier=keyid,issuer:always
# This stuff is for subjectAltName and issuerAltname.
# Import the email address.
# subjectAltName=email:copy
# An alternative to produce certificates that aren't
# deprecated according to PKIX.
# subjectAltName=email:move
# Copy subject details
# issuerAltName=issuer:copy
#nsCaRevocationUrl          = http://www.domain.dom/ca-crl.pem
#nsBaseUrl
#nsRevocationUrl
#nsRenewalUrl
#nsCaPolicyUrl
#nsSslServerName
[ v3_req ]
# Extensions to add to a certificate request
basicConstraints = CA:FALSE
keyUsage = nonRepudiation, digitalSignature, keyEncipherment
[ v3_ca ]
# Extensions for a typical CA
# PKIX recommendation.
subjectKeyIdentifier=hash
authorityKeyIdentifier=keyid:always,issuer:always
# This is what PKIX recommends but some broken software chokes on critical
# extensions.
#basicConstraints = critical,CA:true
# So we do this instead.
basicConstraints = CA:true
# Key usage: this is typical for a CA certificate. However since it will
# prevent it being used as an test self-signed certificate it is best
# left out by default.
# keyUsage = cRLSign, keyCertSign
# Some might want this also
# nsCertType = sslCA, emailCA
# Include email address in subject alt name: another PKIX recommendation
# subjectAltName=email:copy
# Copy issuer details
# issuerAltName=issuer:copy
# DER hex encoding of an extension: beware experts only!
# obj=DER:02:03
# Where 'obj' is a standard or added object
# You can even override a supported extension:
# basicConstraints= critical, DER:30:03:01:01:FF
[ crl_ext ]
# CRL extensions.
# Only issuerAltName and authorityKeyIdentifier make any sense in a CRL.
# issuerAltName=issuer:copy
authorityKeyIdentifier=keyid:always,issuer:always