diff --git a/auto.def b/auto.def
index 1e388ac20e..eee8c5aeff 100644
--- a/auto.def
+++ b/auto.def
@@ -123,7 +123,6 @@ set DUMP_DEFINES_JSON ""; #./config.defines.json
 ########################################################################
 set flags {
   # <build-modes>
-  with-debug:=1        => {Enable debug build flags}
   shared=1             => {Disable build of shared libary}
   static=1             => {Disable build of static library (mostly)}
   amalgamation=1       => {Disable the amalgamation and instead build all files separately.}
@@ -193,10 +192,16 @@ set flags {
   with-emsdk:=auto     => {Top-most dir of the Emscripten SDK installation. Default = EMSDK env var.}
   # </alternative-builds>
   # <developer>
+
+  # --with-debug does more than simply builds with a -g compilation
+  # flag and will impact performance by as much as 4x, as it includes
+  # large numbers of assert()s in performance-critical loops.  Never
+  # use --with-debug for production builds.
+  with-debug:=1        => {Enable debug build flags}
+  dev                  => {Enable dev-mode build: automatically enables certain other flags}
   test-status          => {Enable status of tests}
   gcov=0               => {Enable coverage testing using gcov}
   linemacros           => {Enable #line macros in the amalgamation}
-  dev                  => {Enable dev-mode build: automatically enables certain other flags}
   dump-defines=0       => {Dump autosetup defines to $DUMP_DEFINES_TXT (for build debugging)}
   link-tools-dynamically => {Dynamically link libsqlite3 to certain tools which normally statically embed it.}
   soname:=legacy       => {SONAME for libsqlite3.so. Must be one of: none, auto, legacy}
diff --git a/autosetup/proj.tcl b/autosetup/proj.tcl
index 863962c2f8..7da0b0fa35 100644
--- a/autosetup/proj.tcl
+++ b/autosetup/proj.tcl
@@ -311,11 +311,11 @@ proc proj-first-bin-of {args} {
 ########################################################################
 # @proj-opt-was-provided key
 #
-# Returns 1 if the user specifically provided the given configure
-# flag, else 0. This can be used to distinguish between options which
-# have a default value and those which were explicitly provided by the
-# user, even if the latter is done in a way which uses the default
-# value.
+# Returns 1 if the user specifically provided the given configure flag
+# or if it was specifically set using proj-opt-set, else 0. This can
+# be used to distinguish between options which have a default value
+# and those which were explicitly provided by the user, even if the
+# latter is done in a way which uses the default value.
 #
 # For example, with a configure flag defined like:
 #
diff --git a/main.mk b/main.mk
index af616086be..3193e531d1 100644
--- a/main.mk
+++ b/main.mk
@@ -901,6 +901,9 @@ TESTOPTS = --verbose=file --output=test-out.txt
 #
 # Extra compiler options for various shell tools
 #
+# Note that some of these will only apply when embedding sqlite3.c
+# into the shell, as these flags are not otherwise passed on to the
+# library.
 SHELL_OPT += -DSQLITE_DQS=0
 SHELL_OPT += -DSQLITE_ENABLE_FTS4
 #SHELL_OPT += -DSQLITE_ENABLE_FTS5
@@ -1926,30 +1929,27 @@ threadtest5: sqlite3.c $(TOP)/test/threadtest5.c
 	$(T.link) $(TOP)/test/threadtest5.c sqlite3.c -o $@ $(LDFLAGS.libsqlite3)
 xbin: threadtest5
 
-# The standard CLI is built using the amalgamation since it uses
-# special compile-time options that are interpreted by individual
-# source files within the amalgamation.
 #
-# How/whether we build sqlite3$(T.exe) depends on both
-# $(HAVE_WASI_SDK) and $(LINK_TOOLS_DYNAMICALLY), thus there are
-# several targets here, only one of which the sqlite3$(T.exe) target
-# indirectly resolves to.
+# When building sqlite3$(T.exe) we specifically embed a copy of
+# sqlite3.c, and not link to libsqlite3.so or libsqlite3.a, because
+# the shell needs to be able to enable arbitrary library features,
+# some of which have significant performance impacts. For example,,
+# SQLITE_ENABLE_EXPLAIN_COMMENTS has been measured as having a 5.2%
+# runtime performance hit, which is fine for use in the shell but is
+# not appropriate for the canonical library build.
 #
-sqlite3-shell.0.0.deps = shell.c sqlite3.c
-sqlite3-shell.0.0.rules = \
-    $(T.link) -o $@ \
-        shell.c sqlite3.c \
-        $(CFLAGS.readline) $(SHELL_OPT) $(CFLAGS.icu) \
-        $(LDFLAGS.libsqlite3) $(LDFLAGS.readline)
-sqlite3-shell.0.1.deps = shell.c $(libsqlite3.SO)
-sqlite3-shell.0.1.rules = \
-    $(T.link) -o $@ \
-        shell.c -L. -lsqlite3 \
-        $(CFLAGS.readline) $(SHELL_OPT) $(CFLAGS.icu) \
-        $(LDFLAGS.configure) $(LDFLAGS.readline) $(LDFLAGS.zlib)
-sqlite3$(T.exe): $(sqlite3-shell.$(HAVE_WASI_SDK).$(LINK_TOOLS_DYNAMICALLY).deps)
-	$(sqlite3-shell.$(HAVE_WASI_SDK).$(LINK_TOOLS_DYNAMICALLY).rules)
-all: sqlite3$(T.exe)
+sqlite3$(T.exe):	shell.c sqlite3.c
+	$(T.link) -o $@ \
+		shell.c sqlite3.c \
+		$(CFLAGS.readline) $(SHELL_OPT) $(CFLAGS.icu) \
+		$(LDFLAGS.libsqlite3) $(LDFLAGS.readline)
+#
+# Build sqlite3$(T.exe) by default except in wasi-sdk builds.  Yes, the
+# semantics of 0 and 1 are confusingly swapped here.
+#
+sqlite3$(T.exe)-1:
+sqlite3$(T.exe)-0: sqlite3$(T.exe)
+all: sqlite3$(T.exe)-$(HAVE_WASI_SDK)
 
 # The "sqlite3d" CLI is build using separate source files.  This
 # is useful during development and debugging.
diff --git a/manifest b/manifest
index 3cfb99819a..e7c415ad2b 100644
--- a/manifest
+++ b/manifest
@@ -1,5 +1,5 @@
-C Reformulate\ssqldiff\sdeps\sand\srules\sso\sthat\sthe\starget\smatches\sthe\sresulting\sfile\sname,\sto\savoid\srebuilding\sit\son\severy\smake\sinvocation.\sApply\sthe\ssame\streatment\sto\sthe\ssqlite3\sCLI\sshell.
-D 2024-11-19T16:40:49.154
+C Revert\slinking\sthe\sshell\sto\sthe\sdll\sfor\sreasons\sexplained\sin\snew\smakefile\scomments.\sMove\sthe\s--with-debug\sconfigure\sflag\sinto\sthe\sdeveloper\soptions\sset\sand\sadd\scommentary\sabout\swhy\sit\sshould\snever\sbe\sused\sfor\sproduction\sbuilds.
+D 2024-11-19T17:41:13.115
 F .fossil-settings/empty-dirs dbb81e8fc0401ac46a1491ab34a7f2c7c0452f2f06b54ebb845d024ca8283ef1
 F .fossil-settings/ignore-glob 35175cdfcf539b2318cb04a9901442804be81cd677d8b889fcc9149c21f239ea
 F LICENSE.md e108e1e69ae8e8a59e93c455654b8ac9356a11720d3345df2a4743e9590fb20d
@@ -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 b6fc55bf238320b58d06d6e5364374722aae3b8320c4f928e0e6c208405f2cfd
+F auto.def 4f5ae3ed11bb110b1eda2a6b7ee46489b7371bc8f7c19f0ed944613c170e4951
 F autoconf/INSTALL 83e4a25da9fd053c7b3665eaaaf7919707915903
 F autoconf/Makefile.am adedc1324b6a87fdd1265ddd336d2fb7d4f36a0e77b86ea553ae7cc4ea239347
 F autoconf/Makefile.fallback 22fe523eb36dfce31e0f6349f782eb084e86a5620b2b0b4f84a2d6133f53f5ac
@@ -49,7 +49,7 @@ F autosetup/cc-shared.tcl 4f024e94a47f427ba61de1739f6381ef0080210f9fae89112d5c1d
 F autosetup/cc.tcl c0fcc50ca91deff8741e449ddad05bcd08268bc31177e613a6343bbd1fd3e45f
 F autosetup/jimsh0.c d40e381ea4526a067590e7b91bd4b2efa6d4980d286f908054c647b3df4aee14
 F autosetup/pkg-config.tcl 4e635bf39022ff65e0d5434339dd41503ea48fc53822c9c5bde88b02d3d952ba
-F autosetup/proj.tcl 96fe16b87c9feb9c1cf2682280f678c659bc52c09fca5de02afc2f7ec5bfb154
+F autosetup/proj.tcl 22556a325c964aa5377d4d881722385f41fcd7c1b60102ba8965f7814c83e9ce
 F autosetup/system.tcl 51d4be76cd9a9074704b584e5c9cbba616202c8468cf9ba8a4f8294a7ab1dba9
 F configure 9a00b21dfd13757bbfb8d89b30660a89ec1f8f3a79402b8f9f9b6fc475c3303a x
 F contrib/sqlitecon.tcl 210a913ad63f9f991070821e599d600bd913e0ad
@@ -696,7 +696,7 @@ F ext/wasm/tests/opfs/concurrency/test.js d08889a5bb6e61937d0b8cbb78c9efbefbf65a
 F ext/wasm/tests/opfs/concurrency/worker.js 0a8c1a3e6ebb38aabbee24f122693f1fb29d599948915c76906681bb7da1d3d2
 F ext/wasm/wasmfs.make bc8bb227f35d5bd3863a7bd2233437c37472a0d81585979f058f9b9b503bef35
 F magic.txt 5ade0bc977aa135e79e3faaea894d5671b26107cc91e70783aa7dc83f22f3ba0
-F main.mk 8ef1c08eb0e644df88978d2b1db4e2af9efc430a0fe3dd152d00fa21593fee41
+F main.mk 7cb02ba61e74ccab3ad6775b9207b12c6a26bbe3b2dd280039bc0cd532a52ceb
 F mptest/config01.test 3c6adcbc50b991866855f1977ff172eb6d901271
 F mptest/config02.test 4415dfe36c48785f751e16e32c20b077c28ae504
 F mptest/crash01.test 61e61469e257df0850df4293d7d4d6c2af301421
@@ -2198,8 +2198,8 @@ F tool/version-info.c 3b36468a90faf1bbd59c65fd0eb66522d9f941eedd364fabccd7227350
 F tool/warnings-clang.sh bbf6a1e685e534c92ec2bfba5b1745f34fb6f0bc2a362850723a9ee87c1b31a7
 F tool/warnings.sh 49a486c5069de041aedcbde4de178293e0463ae9918ecad7539eedf0ec77a139
 F tool/win/sqlite.vsix deb315d026cc8400325c5863eef847784a219a2f
-P 9192c146e2898456a6b8ea43a6f02c0227ddce5b584374fbeb2d63bd2ecd5d8c
-R 9e3125f578c182d0fd3f116bcadb353b
+P 9a17b83f859ef14629cb78d8c9af1b3f2493b0c8756bc2ebcf92f0872fb507c3
+R 0effbfea81177717d860b06a74ce79d8
 U stephan
-Z c9c941efe50c477f477a1622a4a0493c
+Z aa386346708361b0b61a6d6560bd2986
 # Remove this line to create a well-formed Fossil manifest.
diff --git a/manifest.uuid b/manifest.uuid
index 5cd2262fb1..2cf57950de 100644
--- a/manifest.uuid
+++ b/manifest.uuid
@@ -1 +1 @@
-9a17b83f859ef14629cb78d8c9af1b3f2493b0c8756bc2ebcf92f0872fb507c3
+7b14309be42be4204c4d30e9741d56d75ab8ec34686791d032612337fe1c4dcf