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Thank Joe. HG Changeset 3178 did it.

Now in order to leverage it, we need new config variables or sys_prefs entries to switch between
the default (current for backwards compatibility) Comapny Name and Company EMail and
the optional User Real name and User EMail
in determining the mail sender name and Reply-to name.
Sys_prefs would be preferable as they can be set on a per company basis. It should be coded to fall back to the other if one is absent.

FA v2.3.14 Mercurial Build 3175 dated 2013-02-01.

Mere deletion of data records is insufficient.
The auto_increment counter has to be reset as well if used.
Hence a TRUNCATE command is better suited for purges.

Also, some of the data should not be purges as they may pertain to
  permissions,
  logical inter-relationships used in code,
  drop-down list and other form element choices,
  sys_prefs choices.

The recomended way: After FA is setup and tweaked (extensions, languages, roles, prefs) the way you want it. take a backup and use it to restore for purges later on. Remember the passwords as well for the restored state.

Safest way is to have your own GIT repo in a local win box. Take a WinMerge2 diff at each change pulled into GIT and upload the diffs alone. Have a set of non-fa-repo code that needs to be matched with changes in their scripts in the fa_repo and then merge carefully. Since such scripts will be only a handful, it might be better off than conflict resolution in HG. By the way IMHO, HG is not very user friendly to the newbie (YMMV). Git is fantastic. GitHub is a fine online store for it.

To make it easier for the community, I place the diffs in the FA Release Announcement posts from time to time. The Wiki has the bash scripts to do a pull and roll up of the bleeding edge HG code. My request for an online HG snapshot enablement in SF has gone unheeded till date.

Please check that the logged in user has an email entry in his record in the users table and then see if the $_SESSION["wa_current_user"]->email gets populated.

Unless we try having both Reply-to in header and using the -f parameter with no error, we cannot include the code in the base repo as it has to ensure that existing installs with no postfix and just sendmail will still work.

Final solution:
1. Fix the reply to header variable as in Post 20 of this thread.
2. Make sure the real_name field in the users table for the logged in use is populated. Otherwise take the fix from Post 25 in this thread.

@ed10: While I was documenting the code trace back to where the variables were set, you beat me to it!

You can actually dump the specific session variable:

echo print_r($_SESSION["wa_current_user"], true);

at the location of the send() and see what is the output!

Line 95 in admin/db/users_db.inc in function get_users_by_login():

$sql = "SELECT * FROM ".TB_PREF."users WHERE user_id=".db_escape($user_id);

Hence all fields must be available and in your instance, the real_name field may not have been set, though in the email instance, the username may be okay.

The said variable:
$_SESSION["wa_current_user"]->name
appears in:

reporting/includes/pdf_report.inc
reporting/includes/excel_report.inc
admin/db/maintenance_db.inc
themes/aqua/renderer.php
themes/cool/renderer.php
themes/default/renderer.php

A few months ago, some repeating code in all the renderer.php files were siphoned out elsewhere to a single function and at that time the variable may have vanished from being set or when changes to includes/session.inc were made over time.

Therefore while retaining the variable $_SESSION["wa_current_user"]->name in the said files, it may be required to set the field real_name from the users table if the user is logged in - in the includes/session.inc file.

Come to think of it, thereal_namein theuserstable does not seem to be used anywhere! Optional field that may not have any value at all!

Line 47 of reporting/includes/class.mail.inc:

$this->header = "From: $name <$mail>\n";

may be replaced with:

$this->header = "From: $name <$mail>\nReply-to: $name <$mail>\n";

The $add_params variable in the class.mail.inc file remains unused. Quote from the PHP manual for mail():

The $this-user in the other files may have an issue of scope of being an included file's variable.

Exchange Rate is 1 for home currency. Recalculate all the others (done by getting the current exchanges rates and adjusting as required) and create currencies you use but are currently absent ad acquire / fix their exchange rates.

It is possible that the comma may be a delimiter somewhere and may need to be stripped out of the Name. Also was checking for consistency and alternatives to the existing mailer like the integration in similar context.

For your specific requirement, you may want to dump the variables just before the send() occurs in both the caller instance and in the class method as well.