Fix many various doc issues.

bin/pt-config-diff

@@ -5453,12 +5453,6 @@ L<"SYNOPSIS"> and usage information for details.
 
 Prompt for a password when connecting to MySQL.
 
-=item --[no]ignore-case
-
-default: yes
-
-Compare the variables case-insensitively.
-
 =item --charset
 
 short form: -A; type: string
@@ -5500,6 +5494,12 @@ short form: -h; type: string
 
 Connect to host.
 
+=item --[no]ignore-case
+
+default: yes
+
+Compare the variables case-insensitively.
+
 =item --ignore-variables
 
 type: array

bin/pt-deadlock-logger

@@ -5181,16 +5181,16 @@ Normally the L<"--dest"> table is expected to exist already.  This option
 causes pt-deadlock-logger to create the table automatically using the suggested
 table structure.
 
+=item --daemonize
+
+Fork to the background and detach from the shell.  POSIX operating systems only.
+
 =item --database
 
 short form: -D; type: string
 
 Connect to this database.
 
-=item --daemonize
-
-Fork to the background and detach from the shell.  POSIX operating systems only.
-
 =item --defaults-file
 
 short form: -F; type: string

bin/pt-fk-error-logger

@@ -4213,16 +4213,16 @@ type: Array
 Read this comma-separated list of config files; if specified, this must be the
 first option on the command line.
 
+=item --daemonize
+
+Fork to the background and detach from the shell.  POSIX operating systems only.
+
 =item --database
 
 short form: -D; type: string
 
 Connect to this database.
 
-=item --daemonize
-
-Fork to the background and detach from the shell.  POSIX operating systems only.
-
 =item --defaults-file
 
 short form: -F; type: string

bin/pt-kill

@@ -7404,12 +7404,6 @@ type: Array
 Read this comma-separated list of config files; if specified, this must be the
 first option on the command line.
 
-=item --database
-
-short form: -D; type: string
-
-The database to use for the connection.
-
 =item --create-log-table
 
 Create the L<"--log-dsn"> table if it does not exist.
@@ -7422,6 +7416,12 @@ default structure shown in the documentation for that option.
 Fork to the background and detach from the shell.  POSIX operating systems
 only.
 
+=item --database
+
+short form: -D; type: string
+
+The database to use for the connection.
+
 =item --defaults-file
 
 short form: -F; type: string

bin/pt-mext

@@ -684,7 +684,7 @@ line at a time.  It places each line into a temporary file.  When it finds a
 blank line, it assumes that a new sample of SHOW GLOBAL STATUS is starting,
 and it creates a new temporary file.  At the end of this process, it has a
 number of temporary files.  It joins the temporary files together side-by-side
-and prints the result.  If the L<"-r"> option is given, it first subtracts
+and prints the result.  If L<"--relative"> option is given, it first subtracts
 each sample from the one after it before printing results.
 
 =head1 OPTIONS

bin/pt-query-digest

@@ -15212,17 +15212,17 @@ Create the L<"--review"> table if it does not exist.
 This option causes the table specified by L<"--review"> to be created
 with the default structure shown in the documentation for L<"--review">.
 
+=item --daemonize
+
+Fork to the background and detach from the shell.  POSIX
+operating systems only.
+
 =item --database
 
 short form: -D; type: string
 
 Connect to this database.
 
-=item --daemonize
-
-Fork to the background and detach from the shell.  POSIX
-operating systems only.
-
 =item --defaults-file
 
 short form: -F; type: string

bin/pt-summary

@@ -2564,17 +2564,23 @@ first option on the command line.
 
 Print help and exit.
 
+=item --read-samples
+
+type: string
+
+Create a report from the files in this directory.
+
 =item --save-samples
 
 type: string
 
 Save the collected data in this directory.
 
-=item --read-samples
+=item --sleep
 
-type: string
+type: int; default: 5
 
-Create a report from the files in this directory.
+How long to sleep when gathering samples from vmstat.
 
 =item --summarize-mounts
 
@@ -2594,18 +2600,16 @@ default: yes; negatable: yes
 
 Report on top processes and C<vmstat> output.
 
-=item --sleep
-
-type: int; default: 5
-
-How long to sleep when gathering samples from vmstat.
-
 =item --version
 
 Print tool's version and exit.
 
 =back
 
+=head1 ENVIRONMENT
+
+This tool does not use any environment variables.
+
 =head1 SYSTEM REQUIREMENTS
 
 This tool requires the Bourne shell (F</bin/sh>).

bin/pt-table-checksum

@@ -11536,11 +11536,11 @@ The number of chunks into which the table was divided.
 
 The number of chunks that were skipped due one or more of these problems:
 
-   * MySQL not using the L<"--chunk-index">
+   * MySQL not using the --chunk-index
-   * MySQL not using the full chunk index (L<"--[no]check-plan">)
+   * MySQL not using the full chunk index (--[no]check-plan)
-   * Chunk size is greater than L<"--chunk-size"> * L<"--chunk-size-limit">
+   * Chunk size is greater than --chunk-size * --chunk-size-limit
-   * Lock wait timeout exceeded (L<"--retries")
+   * Lock wait timeout exceeded (--retries)
-   * Checksum query killed (L<"--retries">)
+   * Checksum query killed (--retries)
 
 As of pt-table-checksum 2.2.5, skipped chunks cause a non-zero L<"EXIT STATUS">.
 

bin/pt-variable-advisor

@@ -5867,12 +5867,6 @@ runs SET NAMES UTF8 after connecting to MySQL.  Any other value sets
 binmode on STDOUT without the utf8 layer, and runs SET NAMES after
 connecting to MySQL.
 
-=item --database
-
-short form: -D; type: string
-
-Connect to this database.
-
 =item --config
 
 type: Array
@@ -5885,6 +5879,12 @@ first option on the command line.
 Fork to the background and detach from the shell.  POSIX
 operating systems only.
 
+=item --database
+
+short form: -D; type: string
+
+Connect to this database.
+
 =item --defaults-file
 
 short form: -F; type: string