Merge upstream SQLite 3.46.1

[penberg]

Updates libSQL's vendored SQLite from 3.45.1 → 3.46.1 (upstream tag version-3.46.1, f3d536d).

Despite libSQL claiming to be 3.46.1 in the version strings, it was based on upstream version 3.45.1 (9ed72eb).

What's in here:

• libsql-sqlite3/ — the vendored SQLite source tree merged up to 3.46.1, with libSQL's modifications preserved (vector indexes, extra pragmas, WASM tweaks, etc.).
• libsql-ffi/bundled/ — regenerated amalgamation (sqlite3.c/sqlite3.h now report SQLITE_VERSION "3.46.1" with the …alt1 libSQL source-id marker) and session_bindgen.rs, via LIBSQL_DEV=1 cargo build --features multiple-ciphers,session. The SQLite3MultipleCiphers fileio.c/series.c were out-of-band synced to match 3.46.1.
• Tooling — scripts/sqlite-diff (diffs only upstream's src/ artifacts between two trees) and scripts/update-sqlite-bundle.sh, so future bumps are reproducible.
• ext/intck/ is new from upstream and was relocated under libsql-sqlite3/ where Makefile.in already expects it.

Conflicts resolved:

• src/pragma.c (integrity_check) — upstream replaced the per-table count loop with a single pre-pass using b-tree counts from OP_IntegrityCk. Took upstream's refactored form and re-added the IsVectorIndex(pIdx) skip in the relocated loop, keeping cnt++ unconditional so aRoot register indexing stays aligned. The existing per-row vector-index skip was untouched.
• src/where.c — kept libSQL's if (pProbe->idxIsVector) opMask = 0; alongside upstream's refined bLowQual && pSrc->fg.isIndexedBy==0 (cherry-pick 626d619); took upstream's WHERE_KEEP_ALL_JOINS (cherry-pick 2fdb323).
• src/shell.c.in — libSQL's .init_wasm_func_table and upstream's new .intck command coexist.
• ext/wasm/GNUmakefile — preserved libSQL's -DSQLITE_OMIT_SHARED_MEM and -lm next to upstream's new SEE filter hook (c-pp preprocessor only; no effect on WASM output).
• tool/mksqlite3c.tcl — kept wasmedge_bindings.c in the amalgamation source list.
• FTS3/FTS5 + mechanical files — taken from upstream; these were merge-base artifacts (base 3.45.0 vs HEAD already at 3.45.1). libSQL's local trigram-tokenizer crash fix (3e56d28) is now superseded by upstream's a751fdd.

How this was verified:

The libsql-sqlite3/src tree was diffed against both clean upstream bases using scripts/sqlite-diff and compared the two patches — they should differ only in context lines and hunk offsets (upstream code that changed between releases), never in libSQL's actual +/- content.

scripts/sqlite-diff <clean-3.45.1> libsql-sqlite3 > libsql-sqlite3-3.45.1.patch
scripts/sqlite-diff <clean-3.46.1> libsql-sqlite3 > libsql-sqlite3-3.46.1.patch

The diffs are the same except for a single divergence is the PRAGMA integrity_check vector-index guard, which is the same libSQL change in two shapes because upstream refactored that loop between releases:

• vs 3.45.1: if( IsVectorIndex(pIdx) ) continue;
• vs 3.46.1: folded into upstream's new check → if( pIdx->pPartIdxWhere==0 && !IsVectorIndex(pIdx) ){

Both skip vector indexes during integrity check — identical semantics. Ground truth confirms the tree is correctly ported (src/pragma.c:1804).

Test plan:

• SQLite TCL test suite