feat: Copy/archive input XML files into the output directory

[kdrienCG]

(Previously #4003)

This PR proposes to archive the XML input deck to the output directory, so that every set of results is accompanied by the exact input that produced it.

When GEOS is run with the new archive command line option (-a LEVEL), all XML input files (and every files that are included via the <Included> XML tag) are flattened into a single file in a timestamped directory.

Following suggestions from @rrsettgast and @bd713, the XML input files are "flattened" into a single XML file.

The following command line argument is added to specifiy the level of archiving wanted:

-a, --archive,  Archiving strategy's level:
                  0 = no archiving,
                  1 = XML inputs only (default),
                  2 = XML inputs and the XSD schema

---

Given a run like:

geosx -i foo.xml -o OUTPUT/ -a 2

The following is created:

.
└─ OUTPUT/   
   └─ archive_inputFiles/
      └─ 20260320_103034/
         ├─ input.xml
         └─ schema.xsd

---

Previous proposition

This PR proposes to automatically archive the XML input deck to the output directory, so that every set of results is accompanied by the exact input that produced it.

When GEOS is run with an output directory specified (-o <dir>), all XML input files (and every files that are included via the <Included> XML tag) are copied into the output directory with a timestamp.

---

Given a run like:

geosx -i foo.xml -o OUTPUT/

The following is created:

.
└─ OUTPUT/   
   └─ archive_inputFiles/
      └─ 20260320_103034/
         ├─ foo.xml
         │
         ├─ include1.xml
         │
         └─ some_subdir/
            └─ include2.xml

When included files are "behind" the input tree of the main XML, the following structure is proposed:

.
└─ OUTPUT/   
   └─ archive_inputFiles/
      └─ 20260320_103034/
         ├─ foo.xml
         │
         ├─ __one_level_behind_include.xml
         │
         ├─ __one_level_behind_folder/           
         |  └─ baz.xml
         │
         └─ ____two_level_behind_folder/      
            └─ buzz.xml

Files outside the input tree (reached via ../) are prefixed with __ for every ../ from foo.xml.

[herve-gross]

@bd713 moving this to the review queue

[bd713]

Thanks, @kdrienCG.

Could you also update the GEOS documentation accordingly?
Typically QuickStart.rst for the new CLI flag, and maybe worth a brief description under Advanced XML Features.

[bd713]

Comma needed to actually construct the 2 candidates.
Otherwise schema archiving always fails in my tests.

Suggested change

	GEOS_SCHEMA_SOURCE_PATH
	GEOS_SCHEMA_SOURCE_PATH,

[bd713]

Are these 2 functions still needed for the current flattening strategy?
If not, I would suggest removing them for now.

[kdrienCG]

removed in 81084b8

[bd713]

This feature will be incredibly useful in our production environment. That said, I would personally keep the existing GEOS default behavior (no archiving) unchanged for regular usage, CI, etc.
Same for example as CSV output, which isn't on by default.