diff --git a/Makefile.in b/Makefile.in
index de59f4aaa8..79154f3fed 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -4,9 +4,7 @@
 # Makefile for SQLITE
 #
 # This makefile is intended to be configured automatically using the
-# configure script. Hand editing may not work as expected because
-# certain blocks are added or removed depending on configure-time
-# information.
+# configure script.
 #
 # The docs for many of its variables are in the primary static
 # makefile, main.mk (which this one includes at runtime).
@@ -18,10 +16,6 @@ all:
 # Known TODOs/FIXMEs/TOIMPROVEs for the autosetup port, in no
 # particular order...
 #
-# - libreadline detection and handling of its -I, -L, and -l flags.
-# These can vary considerably across systems. e.g. some need -lncurses,
-# and some don't know what an -lncurses is.
-#
 # - TEA pieces.
 #
 # - Replace the autotools-specific distribution deliverable(s).
@@ -34,13 +28,6 @@ all:
 # - This makefile should remain as POSIX-make-compatible as possible:
 #   https://pubs.opengroup.org/onlinepubs/9799919799/utilities/make.html
 #
-# - When using the X?=Y variable assignment formulation, please test
-#   the build with both GNU make and a POSIX make (e.g. BSD make,
-#   a.k.a. bmake). On at least one occassion, that formulation has led
-#   to inconsistent behavior between the two major make flavors when
-#   used with variable names which might sensibly be in the
-#   developer's environment (namely CC).
-#
 # - The naming convention of some vars, using periods instead of
 #   underscores, though unconventional, was selected for a couple of
 #   reasons: 1) Personal taste (for which there is no accounting).  2)
@@ -357,16 +344,20 @@ misspell: ./custom.rws has_tclsh84
 # perform cleanup known to be relevant to (only) the autosetup-driven
 # build.
 #
-clean-autosetup:
-	-gmake -C ext/wasm distclean 2>/dev/null || true
-clean: clean-autosetup
+#clean-autosetup:
+#	-if [ -f ext/wasm/GNUmakefile ]; then \
+#		gmake --no-print-directory --ignore-errors -C ext/wasm clean; \
+#	fi >/dev/null 2>&1; true
+#clean: clean-autosetup
 
 distclean-autosetup:	clean
 	rm -f sqlite_cfg.h config.log config.status config.defines.* Makefile sqlite3.pc
 	rm -f $(TOP)/tool/emcc.sh
 	rm -f libsqlite3*$(T.dll)
 	rm -f jimsh0*
-	-gmake -C ext/wasm distclean 2>/dev/null; true
+#	-if [ -f ext/wasm/GNUmakefile ]; then \
+#		gmake --no-print-directory  --ignore-errors -C ext/wasm distclean; \
+#	fi >/dev/null 2>&1; true
 distclean: distclean-autosetup
 
 #
diff --git a/auto.def b/auto.def
index aa3e23e85f..5f751c77f8 100644
--- a/auto.def
+++ b/auto.def
@@ -219,15 +219,14 @@ proj-xfer-options-aliases {
 }
 
 set srcdir $::autosetup(srcdir)
-set top_srcdir [get-define abs_top_srcdir]
-set PACKAGE_VERSION [readfile $srcdir/VERSION]
+set PACKAGE_VERSION [proj-file-content -trim $srcdir/VERSION]
 define PACKAGE_NAME "sqlite"
 define PACKAGE_URL {https://sqlite.org}
 define PACKAGE_VERSION $PACKAGE_VERSION
 define PACKAGE_STRING "[get-define PACKAGE_NAME] $PACKAGE_VERSION"
 define PACKAGE_BUGREPORT [get-define PACKAGE_URL]/forum
-msg-result "srcdir = $srcdir"
-msg-result "top_srcdir = $top_srcdir"
+msg-result "Source dir = $srcdir"
+msg-result "Build dir  = $::autosetup(builddir)"
 msg-result "Configuring SQLite version $PACKAGE_VERSION"
 
 #
@@ -235,7 +234,7 @@ msg-result "Configuring SQLite version $PACKAGE_VERSION"
 # configure script with the same arguments it was initially invoked
 # with. This can be used to automatically reconfigure
 #
-define-append SQLITE_AUTORECONFIG cd '$::autosetup(builddir)' && '$top_srcdir/configure'
+define-append SQLITE_AUTORECONFIG cd '$::autosetup(builddir)' && '$srcdir/configure'
 #{*}$::autosetup(argv) breaks with --flag='val with spaces', so...
 foreach arg $::autosetup(argv) {
   define-append SQLITE_AUTORECONFIG '$arg'
@@ -243,11 +242,6 @@ foreach arg $::autosetup(argv) {
 
 # Are we cross-compiling?
 set isCrossCompiling [proj-is-cross-compiling]
-if {![file exists sqlite3.pc.in]} {
-  msg-result "This appears to be an out-of-tree build."
-}
-
-cc-check-tools ld ar
 
 define OPT_FEATURE_FLAGS {} ; # -DSQLITE_OMIT/ENABLE flags.
 define OPT_SHELL {}         ; # CFLAGS for the sqlite3 CLI app
@@ -297,6 +291,7 @@ if {".exe" eq [get-define TARGET_EXEEXT]} {
 
 #########
 # Programs needed
+cc-check-tools ld ar ; # must come before sqlite-check-wasi-sdk
 if {"" eq [proj-bin-define install]} {
   proj-warn "Cannot find install binary, so 'make install' will not work."
 }
@@ -482,7 +477,7 @@ proc sqlite-check-tcl {} {
     return
   }
   # TODO: document the steps this is taking.
-  global top_srcdir
+  global srcdir
   msg-result "Checking for a suitable tcl... "
   proj-assert {proj-opt-truthy tcl}
   set use_tcl 1
@@ -509,7 +504,7 @@ proc sqlite-check-tcl {} {
       define TCLSH_CMD $with_tclsh
       #msg-result "Using tclsh: $with_tclsh"
     }
-    if {[catch {exec $with_tclsh $top_srcdir/tool/find_tclconfig.tcl} result] == 0} {
+    if {[catch {exec $with_tclsh $srcdir/tool/find_tclconfig.tcl} result] == 0} {
       set with_tcl $result
     }
     if {"" ne $with_tcl && [file isdir $with_tcl]} {
@@ -575,7 +570,7 @@ proc sqlite-check-tcl {} {
   # Export a subset of tclConfig.sh to the current TCL-space.  If the
   # config is not available, this emits empty-string entries for the
   # various options we're interested in.
-  eval [exec "${top_srcdir}/tool/tclConfigShToTcl.sh" "$cfg"]
+  eval [exec "${srcdir}/tool/tclConfigShToTcl.sh" "$cfg"]
 
   if {"" eq $with_tclsh && $cfg ne ""} {
     proj-assert {expr {"" ne [get-define TCL_EXEC_PREFIX]}}
@@ -1202,13 +1197,13 @@ if {0 && "" ne [get-define CFLAGS_JIMSH]} {
 ########################################################################
 # "Re-export" the autoconf-conventional --XYZdir flags into something
 # which is more easily overridable from a make invocation. See the docs
-# for [proj-redirect-autoconf-dir-vars] for the explanation of why.
+# for [proj-remap-autoconf-dir-vars] for the explanation of why.
 #
 # We do this late in the config process, immediately before we export
 # the Makefile and other generated files, so that configure tests
 # which may make use of the autotools-conventional flags
 # (e.g. [proj-check-rpath]) may do so before we "mangle" them here.
-proj-redirect-autoconf-dir-vars
+proj-remap-autoconf-dir-vars
 
 ########################################################################
 # Generate the output files.
@@ -1234,18 +1229,12 @@ if {0} {
 ########################################################################
 # Some build-dev/debug-only output
 proj-if-opt-truthy dump-defines {
-  msg-result "--dump-defines is creating $::DUMP_DEFINES_TXT"
   make-config-header $::DUMP_DEFINES_TXT \
     -bare {SQLITE_OS* SQLITE_DEBUG USE_*} \
     -str {BIN_* CC LD AR LDFLAG* OPT_*} \
     -auto {*}
   # achtung: ^^^^ whichever SQLITE_OS_foo flag which is set to 0 will
   # get _undefined_ here unless it's part of the -bare set.
-  if {0} {
-    foreach x [all-defines] {
-      puts "\t$x"
-    }
-  }
   if {"" ne $DUMP_DEFINES_JSON} {
     msg-result "--dump-defines is creating $::DUMP_DEFINES_JSON"
     ########################################################################
diff --git a/autosetup/proj.tcl b/autosetup/proj.tcl
index 05695ca26a..5f6f083ead 100644
--- a/autosetup/proj.tcl
+++ b/autosetup/proj.tcl
@@ -1083,7 +1083,7 @@ proc proj-which-linenoise {dotH} {
 # configure-time, so would be tedious to override properly via a make
 # invocation.
 #
-proc proj-redirect-autoconf-dir-vars {} {
+proc proj-remap-autoconf-dir-vars {} {
   set prefix [get-define prefix]
   set exec_prefix [get-define exec_prefix $prefix]
   # Note that the ${...} here refers to make-side var derefs, not
diff --git a/manifest b/manifest
index 3c5981fff8..531fd86fad 100644
--- a/manifest
+++ b/manifest
@@ -1,9 +1,9 @@
-C Enhance\sthe\srpath\sconfigure\scheck\sto\shonor\s--exec-prefix=...\sRemove\ssome\sdebugging\scode\sand\smove\sother\sdebugging\scode\saround.
-D 2024-11-05T08:21:47.035
+C auto.def:\sremove\san\sextraneous\sglobal\svar,\ssome\sdead\stcl/makefile\scode/comments,\sand\ssome\sextraneous\soutput.\sRename\san\sinternal-use\sproc.\sDisable\sthe\sext/wasm\scleanup\sin\sthe\stop-level\s(dist)clean\sbecause\sthe\snoise\sfrom\sgmake\sis\sirritating.
+D 2024-11-05T09:49:53.043
 F .fossil-settings/empty-dirs dbb81e8fc0401ac46a1491ab34a7f2c7c0452f2f06b54ebb845d024ca8283ef1
 F .fossil-settings/ignore-glob 35175cdfcf539b2318cb04a9901442804be81cd677d8b889fcc9149c21f239ea
 F LICENSE.md c5b4009dca54d127d2d6033c22fd9cc34f53bedb6ef12c7cbaa468381c74ab28
-F Makefile.in 66cd5f5b89e6f21f7475fd6cd34008c8cd1ec773f22c4aa7f7eafd3ca3634fe9
+F Makefile.in 3a54957d16c3f4666922f170a19b4b51dc13be039c29394dd38caa95ade5d731
 F Makefile.linux-generic bd3e3cacd369821a6241d4ea1967395c962dfe3057e38cb0a435cee0e8b789d0
 F Makefile.msc a92237976eb92c5efaa0dd2524746aec12c196e12df8d4dbff9543a4648c3312
 F README.md c3c0f19532ce28f6297a71870f3c7b424729f0e6d9ab889616d3587dd2332159
@@ -13,7 +13,7 @@ F art/icon-80x90.gif 65509ce3e5f86a9cd64fe7fca2d23954199f31fe44c1e09e208c80fb83d
 F art/sqlite370.eps aa97a671332b432a54e1d74ff5e8775be34200c2
 F art/sqlite370.ico af56c1d00fee7cd4753e8631ed60703ed0fc6e90
 F art/sqlite370.jpg d512473dae7e378a67e28ff96a34da7cb331def2
-F auto.def 3f6aec871699bc3e54f7dc6f4496daf4b435d4b8326bfed51ccabd12b633988c
+F auto.def ac7dfc51216c6aa7d34e82d73c945cb71758a3fb79612ef2c5ed38f468d980e8
 F autoconf/INSTALL 83e4a25da9fd053c7b3665eaaaf7919707915903
 F autoconf/Makefile.am adedc1324b6a87fdd1265ddd336d2fb7d4f36a0e77b86ea553ae7cc4ea239347
 F autoconf/Makefile.fallback 22fe523eb36dfce31e0f6349f782eb084e86a5620b2b0b4f84a2d6133f53f5ac
@@ -49,7 +49,7 @@ F autosetup/cc.tcl c0fcc50ca91deff8741e449ddad05bcd08268bc31177e613a6343bbd1fd3e
 F autosetup/default.auto 5cdf016de2140e50f1db190a02039dc42fb390af1dda4cc4853e3042a9ef0e82
 F autosetup/jimsh0.c d40e381ea4526a067590e7b91bd4b2efa6d4980d286f908054c647b3df4aee14
 F autosetup/pkg-config.tcl 4e635bf39022ff65e0d5434339dd41503ea48fc53822c9c5bde88b02d3d952ba
-F autosetup/proj.tcl 16138ac9c8bc071613b260a18f46ada9a31ed3b496a7ae6f403fd9d49d588aea
+F autosetup/proj.tcl f4762bc4826f3b378bef71236643413c501d537be7320cbc3a163752b1f90964
 F autosetup/system.tcl 51d4be76cd9a9074704b584e5c9cbba616202c8468cf9ba8a4f8294a7ab1dba9
 F autosetup/tmake.auto eaebc74ad538dfdd3c817c27eefc31930c20510c4f3a3704071f6cb0629ed71f
 F autosetup/tmake.tcl a275793ec1b6f8708179af0acef1f6f10d46c2920739743f7a8720c6d700c7a9
@@ -2199,8 +2199,8 @@ F tool/version-info.c 3b36468a90faf1bbd59c65fd0eb66522d9f941eedd364fabccd7227350
 F tool/warnings-clang.sh bbf6a1e685e534c92ec2bfba5b1745f34fb6f0bc2a362850723a9ee87c1b31a7
 F tool/warnings.sh 49a486c5069de041aedcbde4de178293e0463ae9918ecad7539eedf0ec77a139
 F tool/win/sqlite.vsix deb315d026cc8400325c5863eef847784a219a2f
-P af79d11e389b4772a401f6c2cbde42de95287addf7077ad4db55d39cc504f9fe
-R 8f4205f94f3bfdb54022edc4daed40c7
+P a8c1a82b56412a4277a3c9bf2b256d3bd22bd8aca9096b8d08fcc0bf7d9364cb
+R 486858acf83a0ad9398b7511ee6bf899
 U stephan
-Z 23df65f4992f1d4489c83b5031514bec
+Z 17b7f42f98ea7458ea07b6ef75ca0d94
 # Remove this line to create a well-formed Fossil manifest.
diff --git a/manifest.uuid b/manifest.uuid
index a0e57dacbc..2aaf46d2a2 100644
--- a/manifest.uuid
+++ b/manifest.uuid
@@ -1 +1 @@
-a8c1a82b56412a4277a3c9bf2b256d3bd22bd8aca9096b8d08fcc0bf7d9364cb
+ee9eb8b157c93b33a8ac201c31169cdd1d2cf2f21da92f7a6a418a41e5a50b7b