Restructure the pipeline into measure, author and compile

[johnathanchiu]

The module map listed ten modules numbered 0–9, then noted they "are not ten
sequential parts of the pipeline". This groups them into the three phases a run
passes through, and moves the packages to match.

Moves, renames and docs. No logic changes: 613 passed, 2 skipped, the same as
before.

The phases

• measure — establish what the room contains: scene understanding, image
  selection, object merging, grouping.
• author — produce an asset for every measured object: the layout agent,
  object reconstruction.
• compile — link the authored assets into one deliverable scene: room
  definition, QC checks, integration, simulation export.
• across every phase — agent tools, harness, viewing and telemetry, editing.

Phases depend forwards only: author reads what measure established,
compile reads what author produced, nothing reads backwards.

The package moves

pipeline/scene_init/ingest, layout, {artifacts,flow,paths}.py  ->  pipeline/measure/
pipeline/scene_init/reconstruct, seed.py                       ->  pipeline/author/
pipeline/realism_authoring/author                              ->  pipeline/author/realism
pipeline/realism_authoring/live                                ->  pipeline/author/live
pipeline/room_qc/publish                                       ->  pipeline/compile/publish
pipeline/room_qc                                               ->  pipeline/compile/quality_check
pipeline/simulate                                              ->  pipeline/compile/simulate
pipeline/author/reconstruct/mesh_qc                            ->  .../mesh_quality_check
src/litereality_agent                                          ->  src/lrauthor

scene_init spanned two phases — ingest and layout establish what the room
contains, reconstruct and seed produce assets — so splitting it is the point of
the move, and why stages.py now imports ingest from measure and reconstruct
and seed from author.

realism_authoring/author becomes author/realism: the package is the realism
pass over an authored room, and author/author would have said nothing. qc is
spelled out so the two layers read as a pair — mesh_quality_check gates one
object, quality_check gates the assembled room.

The package rename is the import path only. The distribution name
(litereality-agent) and the litereality console script are what users type
and are unchanged.

Docs

doc/ becomes docs/, and assets/doc/ follows it. Directory names are
lowercase so a link is guessable from a module name, and the sim-ready pages
move out of Sim-Ready-intergration/, which was misspelled. Every page is now
linked from modules.md; four were not before.

integration/metadata.md was a stub of notes and is now a reference for the
format properties.py actually writes: the sidecar's fields, that lengths are
metres and everything is Z-up, why colliders are convex, and why density is per
cubic metre of the bounding box rather than of the mesh. What is not covered —
how an object is fixed to a wall — says so.

The numbers are gone from the map. They implied a sequence the doc itself
denied, and a name is stabler to reference than a position in a list. Three
modules were never stages: Agent tools and Harness are used by every phase that
runs a model, which is what makes the harness swappable, and Editing happens
after a run finishes. One module split — the Layout agent was both merging
objects built into each other and making the layout simulation-ready; the first
becomes Object merging under measure, where merge_boxes.py already lives.

Two things a path-based config hid

ruff's extend-exclude named the vendored preprocessing tree by its old path,
so the move silently un-ignored it and produced twelve lint errors that looked
like new bugs. The Modal deploy apps pass the package name as a string to
add_local_python_source("litereality_agent"), which fails at deploy time
rather than import time. Both repointed.

Not in this PR

The run directory layout still uses the old names — <scan>/scene_init/obj_stage,
<scan>/realism_authoring/room. Renaming those changes where artifacts live, so
a scan already on disk stops resuming and re-runs its stages. That wants a
compatibility fallback and its own PR.