fix(server): repair installs that skipped the default-thread-env-mode column

[rynfar]

An earlier build shipped ProjectionThreadSessionLifecycle as migration 41.
This branch later settled on 41 = ProjectionProjectsDefaultThreadEnvMode,
42 = ProjectionProjectFaviconPath, 43 = session lifecycle.

The runner only applies ids above the highest one a database records, so a
database written by that earlier build reports 41 as done, runs 42 and 43, and
never runs 41 — leaving projection_projects without
default_thread_env_mode.

That is not a cosmetic gap. Every project query then fails with no such column, which takes the server down during startup. I hit this against a real
~/.pylon-code database while verifying something else:

INFO: Migrations ran successfully
  migrations: [ '42_ProjectionProjectFaviconPath', '43_ProjectionThreadSessionLifecycle' ]
ERROR: PersistenceSqlError: ... listProjects ... no such column: default_thread_env_mode
Failed running 'src/bin.ts'

Anyone upgrading an install from around that build hits it on first launch.

The fix

Renumbering is what caused this, so the fix cannot be another renumber — those
databases would still skip whatever sits below their high water mark. Migration
44 sits above it and re-adds the column, guarded by a table_info check so
a correctly migrated database is untouched.

Verification

Two unit tests: one reproduces the skip (stop at 40, claim 41, run through 43,
assert the column is missing, then run 44 and assert it is back), one asserts a
correctly migrated database is unchanged.

End to end against a copy of the real database that crashed: it now applies
44_RepairProjectsDefaultThreadEnvMode, starts with zero errors, and keeps its
4 projects and 25 threads.

Server typecheck and lint clean; all 12 migration test files pass.

Also corrects two lines in docs/user/install.md that read "installs beside
Pylon" and "Pylon continues using its own .t3" — both meant T3 Code, from an
over-eager rename. Noticed while following that doc to build a DMG.

Claude Opus 5 (1M context) in Claude Code.

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[github-actions]

Thread transfer impact

⚠️ The latest CI run did not produce a thread transfer result for 6ed91c0.

This comment will update automatically after the next completed run.