diff --git a/auto.def b/auto.def
index 7d67ad7675..aa3e23e85f 100644
--- a/auto.def
+++ b/auto.def
@@ -217,12 +217,6 @@ proj-xfer-options-aliases {
   with-readline-inc => with-readline-cflags
   with-readline-lib => with-readline-ldflags
 }
-#
-# "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.
-#
-proj-redirect-autoconf-dir-vars
 
 set srcdir $::autosetup(srcdir)
 set top_srcdir [get-define abs_top_srcdir]
@@ -1204,6 +1198,18 @@ if {0 && "" ne [get-define CFLAGS_JIMSH]} {
   define-append CFLAGS_JIMSH -DHAVE_LONG_LONG; # SQLite relies on long long, so we know it's available
 }; # JimTCL
 
+
+########################################################################
+# "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.
+#
+# 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
+
 ########################################################################
 # Generate the output files.
 #
@@ -1224,30 +1230,6 @@ if {0} {
     -none *
   proj-touch sqlite_cfg.h ; # help avoid frequent unnecessary @SQLITE_AUTORECONFIG@
 }
-#TODO proj-make-from-dot-in ext/wasm/GNUmakefile
-
-if {"" ne $DUMP_DEFINES_JSON} {
-  ########################################################################
-  # Dump config-defines.json...
-  # Demonstrate (mis?)handling of spaces in JSON-export array values:
-  # define-append OPT_FOO.list {"-DFOO=bar baz" -DBAR="baz barre"}
-  define OPT_FEATURE_FLAGS.list [get-define OPT_FEATURE_FLAGS]
-  define OPT_SHELL.list [get-define OPT_SHELL]
-  set dumpDefsOpt {
-    -bare {SIZEOF_* HAVE_DECL_*}
-    -none {HAVE_CFLAG_* LDFLAGS_* SH_* SQLITE_AUTORECONFIG TARGET_* USE_GCOV TCL_*}
-    -array {*.list}
-    -auto {OPT_* PACKAGE_* HAVE_*}
-  }
-  if {[opt-bool defines-json-include-lowercase]} {
-    lappend dumpDefsOpt -none {lib_*} ; # remnants from proj-check-function-in-lib and friends
-    lappend dumpDefsOpt -auto {[a-z]*}
-  }
-  lappend dumpDefsOpt -none *
-  proj-dump-defs-json $DUMP_DEFINES_JSON {*}$dumpDefsOpt
-  undefine OPT_FEATURE_FLAGS.list
-  undefine OPT_SHELL.list
-}
 
 ########################################################################
 # Some build-dev/debug-only output
@@ -1264,4 +1246,27 @@ proj-if-opt-truthy dump-defines {
       puts "\t$x"
     }
   }
+  if {"" ne $DUMP_DEFINES_JSON} {
+    msg-result "--dump-defines is creating $::DUMP_DEFINES_JSON"
+    ########################################################################
+    # Dump config-defines.json...
+    # Demonstrate (mis?)handling of spaces in JSON-export array values:
+    # define-append OPT_FOO.list {"-DFOO=bar baz" -DBAR="baz barre"}
+    define OPT_FEATURE_FLAGS.list [get-define OPT_FEATURE_FLAGS]
+    define OPT_SHELL.list [get-define OPT_SHELL]
+    set dumpDefsOpt {
+      -bare {SIZEOF_* HAVE_DECL_*}
+      -none {HAVE_CFLAG_* LDFLAGS_* SH_* SQLITE_AUTORECONFIG TARGET_* USE_GCOV TCL_*}
+      -array {*.list}
+      -auto {OPT_* PACKAGE_* HAVE_*}
+    }
+    if {[opt-bool defines-json-include-lowercase]} {
+      lappend dumpDefsOpt -none {lib_*} ; # remnants from proj-check-function-in-lib and friends
+      lappend dumpDefsOpt -auto {[a-z]*}
+    }
+    lappend dumpDefsOpt -none *
+    proj-dump-defs-json $DUMP_DEFINES_JSON {*}$dumpDefsOpt
+    undefine OPT_FEATURE_FLAGS.list
+    undefine OPT_SHELL.list
+  }
 }
diff --git a/autosetup/proj.tcl b/autosetup/proj.tcl
index eee526dea6..05695ca26a 100644
--- a/autosetup/proj.tcl
+++ b/autosetup/proj.tcl
@@ -790,16 +790,18 @@ proc proj-check-emsdk {} {
 # flag. Defines LDFLAGS_RPATH to that/those flag(s) or an empty
 # string. Returns 1 if it finds an option, else 0.
 #
-# By default, the rpath is set to $prefix/lib. However, if
-# --libdir=...  is explicitly passed to configure then that value is
-# used.
+# By default, the rpath is set to $prefix/lib. However, if either of
+# --exec-prefix=... or --libdir=...  are explicitly passed to
+# configure then [get-define libdir] is used (noting that it derives
+# from exec-prefix by default).
 #
 # Achtung: we have seen platforms which report that a given option
 # checked here will work but then fails at build-time, and the current
 # order of checks reflects that.
 proc proj-check-rpath {} {
   set rc 1
-  if {[proj-opt-was-provided libdir]} {
+  if {[proj-opt-was-provided libdir]
+      || [proj-opt-was-provided exec-prefix]} {
     set lp "[get-define libdir]"
   } else {
     set lp "[get-define prefix]/lib"
@@ -1090,7 +1092,6 @@ proc proj-redirect-autoconf-dir-vars {} {
   # [subst] command. i.e. they must use the form ${X}.
   foreach {flag makeVar makeDeref} {
     exec-prefix     exec_prefix    ${prefix}
-    libdir          libdir         ${exec_prefix}/lib
     datadir         datadir        ${prefix}/share
     mandir          mandir         ${datadir}/man
     includedir      includedir     ${prefix}/include
@@ -1104,15 +1105,11 @@ proc proj-redirect-autoconf-dir-vars {} {
     infodir         infodir        ${datadir}/info
     libexecdir      libexecdir     ${exec_prefix}/libexec
   } {
-    # puts "flag=$flag var=$makeVar makeDeref=$makeDeref"
     if {[proj-opt-was-provided $flag]} {
-      #set x "+"
       define $makeVar [opt-val $flag]
     } else {
-      #set x "~"
       define $makeVar $makeDeref
     }
-    #puts "$x $makeVar = [get-define $makeVar]"
   }
 }
 
diff --git a/manifest b/manifest
index 7e9a7e6d58..3c5981fff8 100644
--- a/manifest
+++ b/manifest
@@ -1,5 +1,5 @@
-C Roll\sback\s[47e50fa84dacf83c]\sfor\sconsistency\swith\sthe\slegacy\sbuild.\ssqlite3.pc\sis\snow\sgenerated\sequivalently\sto\sprior\sversions.
-D 2024-11-05T08:14:27.481
+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
 F .fossil-settings/empty-dirs dbb81e8fc0401ac46a1491ab34a7f2c7c0452f2f06b54ebb845d024ca8283ef1
 F .fossil-settings/ignore-glob 35175cdfcf539b2318cb04a9901442804be81cd677d8b889fcc9149c21f239ea
 F LICENSE.md c5b4009dca54d127d2d6033c22fd9cc34f53bedb6ef12c7cbaa468381c74ab28
@@ -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 dd8555a00b22645f0ec06bde38f36fb4a9625fb2ce0950d79dc13c3051f242d1
+F auto.def 3f6aec871699bc3e54f7dc6f4496daf4b435d4b8326bfed51ccabd12b633988c
 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 0bcced417a59fc56da5e6cc6a83e10cca4e10710c0f2f1ae9bc82b366d17699d
+F autosetup/proj.tcl 16138ac9c8bc071613b260a18f46ada9a31ed3b496a7ae6f403fd9d49d588aea
 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 6c6fa3adfee6ec2c57dc76461e7c97416b4fad45772ce367d223cc67e66049f6
-R 91f8f712e56b95f1d0840a661628f372
+P af79d11e389b4772a401f6c2cbde42de95287addf7077ad4db55d39cc504f9fe
+R 8f4205f94f3bfdb54022edc4daed40c7
 U stephan
-Z 5ec50233ebe03347ef3d5c1ede9ca068
+Z 23df65f4992f1d4489c83b5031514bec
 # Remove this line to create a well-formed Fossil manifest.
diff --git a/manifest.uuid b/manifest.uuid
index 00a2ccce48..a0e57dacbc 100644
--- a/manifest.uuid
+++ b/manifest.uuid
@@ -1 +1 @@
-af79d11e389b4772a401f6c2cbde42de95287addf7077ad4db55d39cc504f9fe
+a8c1a82b56412a4277a3c9bf2b256d3bd22bd8aca9096b8d08fcc0bf7d9364cb