diff --git a/doc b/doc
index 610494461f..c78d4a247a 160000
--- a/doc
+++ b/doc
@@ -1 +1 @@
-Subproject commit 610494461fad4ea630c4d31bb30f8bab141da167
+Subproject commit c78d4a247a05b47365f3f2e08cfd62b539f6bcbe
diff --git a/scripts/base/frameworks/broker/main.zeek b/scripts/base/frameworks/broker/main.zeek
index 2990f3f297..21d3cdaf74 100644
--- a/scripts/base/frameworks/broker/main.zeek
+++ b/scripts/base/frameworks/broker/main.zeek
@@ -83,12 +83,12 @@ export {
 	const log_batch_interval = 1sec &redef;
 
 	## Max number of threads to use for Broker/CAF functionality.  The
-	## ZEEK_BROKER_MAX_THREADS environment variable overrides this setting.
+	## ``ZEEK_BROKER_MAX_THREADS`` environment variable overrides this setting.
 	const max_threads = 1 &redef;
 
 	## Max number of items we buffer at most per peer. What action to take when
 	## the buffer reaches its maximum size is determined by
-	## `peer_overflow_policy`.
+	## :zeek:see:`Broker::peer_overflow_policy`.
 	const peer_buffer_size = 2048 &redef;
 
 	## Configures how Broker responds to peers that cannot keep up with the
@@ -98,10 +98,10 @@ export {
 	## - drop_oldest: removed the olsted message from the buffer, then append
 	const peer_overflow_policy = "disconnect" &redef;
 
-	## Same as `peer_buffer_size` but for WebSocket clients.
+	## Same as :zeek:see:`Broker::peer_buffer_size` but for WebSocket clients.
 	const web_socket_buffer_size = 512 &redef;
 
-	## Same as `peer_overflow_policy` but for WebSocket clients.
+	## Same as :zeek:see:`Broker::peer_overflow_policy` but for WebSocket clients.
 	const web_socket_overflow_policy = "disconnect" &redef;
 
 	## The CAF scheduling policy to use.  Available options are "sharing" and
diff --git a/scripts/base/frameworks/input/main.zeek b/scripts/base/frameworks/input/main.zeek
index 973661f871..b1fa455a18 100644
--- a/scripts/base/frameworks/input/main.zeek
+++ b/scripts/base/frameworks/input/main.zeek
@@ -24,10 +24,10 @@ export {
 		STREAM = 2
 	};
 
-	## The default input reader used. Defaults to `READER_ASCII`.
+	## The default input reader used. Defaults to :zeek:see:`Input::READER_ASCII`.
 	option default_reader = READER_ASCII;
 
-	## The default reader mode used. Defaults to `MANUAL`.
+	## The default reader mode used. Defaults to :zeek:see:`Input::MANUAL`.
 	option default_mode = MANUAL;
 
 	## Separator between fields.
@@ -60,7 +60,7 @@ export {
 		# Common definitions for tables and events
 
 		## String that allows the reader to find the source of the data.
-		## For `READER_ASCII`, this is the filename.
+		## For :zeek:see:`Input::READER_ASCII`, this is the filename.
 		source: string;
 
 		## Reader to use for this stream.
@@ -112,7 +112,7 @@ export {
 		##
 		## The event is raised like if it had been declared as follows:
 		## error_ev: function(desc: TableDescription, message: string, level: Reporter::Level) &optional;
-		## The actual declaration uses the ``any`` type because of deficiencies of the Zeek type system.
+		## The actual declaration uses the :zeek:type:`any` type because of deficiencies of the Zeek type system.
 		error_ev: any &optional;
 
 		## A key/value table that will be passed to the reader.
@@ -126,7 +126,7 @@ export {
 		# Common definitions for tables and events
 
 		## String that allows the reader to find the source.
-		## For `READER_ASCII`, this is the filename.
+		## For :zeek:see:`Input::READER_ASCII`, this is the filename.
 		source: string;
 
 		## Reader to use for this stream.
@@ -151,8 +151,8 @@ export {
 		want_record: bool &default=T;
 
 		## The event that is raised each time a new line is received from the
-		## reader. The event will receive an Input::EventDescription record
-		## as the first argument, an Input::Event enum as the second
+		## reader. The event will receive an :zeek:see:`Input::EventDescription` record
+		## as the first argument, an :zeek:see:`Input::Event` enum as the second
 		## argument, and the fields (as specified in *fields*) as the following
 		## arguments (this will either be a single record value containing
 		## all fields, or each field value as a separate argument).
@@ -161,12 +161,12 @@ export {
 		## Error event that is raised when an information, warning or error
 		## is raised by the input stream. If the level is error, the stream will automatically
 		## be closed.
-		## The event receives the Input::EventDescription as the first argument, the
-		## message as the second argument and the Reporter::Level as the third argument.
+		## The event receives the :zeek:see:`Input::EventDescription` as the first argument, the
+		## message as the second argument and the :zeek:see:`Reporter::Level` as the third argument.
 		##
 		## The event is raised like it had been declared as follows:
 		## error_ev: function(desc: EventDescription, message: string, level: Reporter::Level) &optional;
-		## The actual declaration uses the ``any`` type because of deficiencies of the Zeek type system.
+		## The actual declaration uses the :zeek:type:`any` type because of deficiencies of the Zeek type system.
 		error_ev: any &optional;
 
 		## A key/value table that will be passed to the reader.
@@ -179,7 +179,7 @@ export {
 	## file analysis framework.
 	type AnalysisDescription: record {
 		## String that allows the reader to find the source.
-		## For `READER_ASCII`, this is the filename.
+		## For :zeek:see:`Input::READER_ASCII`, this is the filename.
 		source: string;
 
 		## Reader to use for this stream.  Compatible readers must be
@@ -205,14 +205,14 @@ export {
 
 	## Create a new table input stream from a given source.
 	##
-	## description: `TableDescription` record describing the source.
+	## description: :zeek:see:`Input::TableDescription` record describing the source.
 	##
 	## Returns: true on success.
 	global add_table: function(description: Input::TableDescription) : bool;
 
 	## Create a new event input stream from a given source.
 	##
-	## description: `EventDescription` record describing the source.
+	## description: :zeek:see:`Input::EventDescription` record describing the source.
 	##
 	## Returns: true on success.
 	global add_event: function(description: Input::EventDescription) : bool;
@@ -278,4 +278,3 @@ function force_update(id: string) : bool
 	{
 	return __force_update(id);
 	}
-
diff --git a/scripts/base/frameworks/logging/main.zeek b/scripts/base/frameworks/logging/main.zeek
index 953b6a51de..b9f46f4aae 100644
--- a/scripts/base/frameworks/logging/main.zeek
+++ b/scripts/base/frameworks/logging/main.zeek
@@ -198,12 +198,12 @@ export {
 
 	## Default separator for log field scopes when logs are unrolled and
 	## flattened.  This will be the string between field name components.
-	## For example, setting this to "_" will cause the typical field
-	## "id.orig_h" to turn into "id_orig_h".
+	## For example, setting this to ``_`` will cause the typical field
+	## ``id.orig_h`` to turn into ``id_orig_h``.
 	const default_scope_sep = "." &redef;
 
 	## A prefix for extension fields which can be optionally prefixed
-	## on all log lines by setting the `ext_func` field in the
+	## on all log lines by setting the ``ext_func`` field in the
 	## log filter.
 	const Log::default_ext_prefix: string = "_" &redef;
 
diff --git a/scripts/base/frameworks/notice/main.zeek b/scripts/base/frameworks/notice/main.zeek
index d6e43b7357..26b3c1b9d0 100644
--- a/scripts/base/frameworks/notice/main.zeek
+++ b/scripts/base/frameworks/notice/main.zeek
@@ -203,7 +203,7 @@ export {
 	## on rotation with :zeek:enum:`Notice::ACTION_ALARM`.
 	##
 	## Note that this is overridden by the ZeekControl MailTo option or by
-	## the `email_dest` field in the :zeek:see:`Notice::Info` record.
+	## the ``email_dest`` field in the :zeek:see:`Notice::Info` record.
 	const mail_dest           = ""                   &redef;
 
 	## Address that emails will be from.
diff --git a/scripts/base/frameworks/spicy/init-bare.zeek b/scripts/base/frameworks/spicy/init-bare.zeek
index a9f9d2dbd7..e01f4adafd 100644
--- a/scripts/base/frameworks/spicy/init-bare.zeek
+++ b/scripts/base/frameworks/spicy/init-bare.zeek
@@ -23,7 +23,7 @@ export {
 # doc-options-end
 
 # doc-types-start
-    ## Result type for `Spicy::resource_usage()`. The values reflect resource
+    ## Result type for :zeek:see:`Spicy::resource_usage`. The values reflect resource
     ## usage as reported by the Spicy runtime system.
     type ResourceUsage: record {
         user_time : interval;           ##< user CPU time of the Zeek process
diff --git a/scripts/base/frameworks/supervisor/api.zeek b/scripts/base/frameworks/supervisor/api.zeek
index e3a6d06c9b..c53988967a 100644
--- a/scripts/base/frameworks/supervisor/api.zeek
+++ b/scripts/base/frameworks/supervisor/api.zeek
@@ -135,7 +135,7 @@ export {
 	global node: function(): NodeConfig;
 
 	## Hooks into the stdout stream for all supervisor's child processes.
-	## If a hook terminates with `break`, that will suppress output to the
+	## If a hook terminates with ``break``, that will suppress output to the
 	## associated stream.
 	##
 	## node: the name of a previously created node via
@@ -149,7 +149,7 @@ export {
 	global stdout_hook: hook(node: string, msg: string);
 
 	## Hooks into the stderr stream for all supervisor's child processes.
-	## If a hook terminates with `break`, that will suppress output to the
+	## If a hook terminates with ``break``, that will suppress output to the
 	## associated stream.
 	##
 	## node: the name of a previously created node via
diff --git a/scripts/base/frameworks/telemetry/main.zeek b/scripts/base/frameworks/telemetry/main.zeek
index 9c255cb40c..2480cd4b88 100644
--- a/scripts/base/frameworks/telemetry/main.zeek
+++ b/scripts/base/frameworks/telemetry/main.zeek
@@ -42,8 +42,8 @@ export {
 	global counter_with: function(cf: CounterFamily,
 	                              label_values: labels_vector &default=vector()): Counter;
 
-	## Increment a :zeek:see:`Telemetry::Counter` by `amount`.
-	## Using a negative `amount` is an error.
+	## Increment a :zeek:see:`Telemetry::Counter` by ``amount``.
+	## Using a negative ``amount`` is an error.
 	##
 	## c: The counter instance.
 	##
@@ -52,7 +52,7 @@ export {
 	## Returns: True if the counter was incremented successfully.
 	global counter_inc: function(c: Counter, amount: double &default=1.0): bool;
 
-	## Helper to set a :zeek:see:`Telemetry::Counter` to the given `value`.
+	## Helper to set a :zeek:see:`Telemetry::Counter` to the given ``value``.
 	## This can be useful for mirroring counter metrics in an
 	## :zeek:see:`Telemetry::sync` hook implementation.
 	## Setting a value that is less than the current value of the
@@ -126,7 +126,7 @@ export {
 	global gauge_with: function(gf: GaugeFamily,
 	                            label_values: labels_vector &default=vector()): Gauge;
 
-	## Increment a :zeek:see:`Telemetry::Gauge` by `amount`.
+	## Increment a :zeek:see:`Telemetry::Gauge` by ``amount``.
 	##
 	## g: The gauge instance.
 	##
@@ -135,7 +135,7 @@ export {
 	## Returns: True if the gauge was incremented successfully.
 	global gauge_inc: function(g: Gauge, amount: double &default=1.0): bool;
 
-	## Decrement a :zeek:see:`Telemetry::Gauge` by `amount`.
+	## Decrement a :zeek:see:`Telemetry::Gauge` by ``amount``.
 	##
 	## g: The gauge instance.
 	##
@@ -144,7 +144,7 @@ export {
 	## Returns: True if the gauge was incremented successfully.
 	global gauge_dec: function(g: Gauge, amount: double &default=1.0): bool;
 
-	## Helper to set a :zeek:see:`Telemetry::Gauge` to the given `value`.
+	## Helper to set a :zeek:see:`Telemetry::Gauge` to the given ``value``.
 	##
 	## g: The gauge instance.
 	##
@@ -153,7 +153,7 @@ export {
 	## Returns: True if the gauge value was set successfully.
 	global gauge_set: function(g: Gauge, value: double): bool;
 
-	## Increment a :zeek:see:`Telemetry::Gauge` by the given `amount` through
+	## Increment a :zeek:see:`Telemetry::Gauge` by the given ``amount`` through
 	## the :zeek:see:`Telemetry::GaugeFamily`.
 	## This is a short-cut for :zeek:see:`Telemetry::gauge_inc`.
 	## Using a negative amount is an error.
@@ -169,7 +169,7 @@ export {
 	                                  label_values: labels_vector &default=vector(),
 	                                  amount: double &default=1.0): bool;
 
-	## Decrement a :zeek:see:`Telemetry::Gauge` by the given `amount` through
+	## Decrement a :zeek:see:`Telemetry::Gauge` by the given ``amount`` through
 	## the :zeek:see:`Telemetry::GaugeFamily`.
 	## This is a short-cut for :zeek:see:`Telemetry::gauge_dec`.
 	##
@@ -184,7 +184,7 @@ export {
 	                                  label_values: labels_vector &default=vector(),
 	                                  amount: double &default=1.0): bool;
 
-	## Set a :zeek:see:`Telemetry::Gauge` to the given `value` through
+	## Set a :zeek:see:`Telemetry::Gauge` to the given ``value`` through
 	## the :zeek:see:`Telemetry::GaugeFamily`.
 	## This is a short-cut for :zeek:see:`Telemetry::gauge_set`.
 	##
diff --git a/scripts/base/misc/version.zeek b/scripts/base/misc/version.zeek
index 36d8ab1fc3..475593760f 100644
--- a/scripts/base/misc/version.zeek
+++ b/scripts/base/misc/version.zeek
@@ -1,6 +1,6 @@
-##! Provide information about the currently running Zeek version.
-##! The most convenient way to access this are the Version::number
-##! and Version::info constants.
+##! Provide information about the currently running Zeek version.  The most
+##! convenient way to access this are the :zeek:see:`Version::number` and
+##! :zeek:see:`Version::info` constants.
 
 module Version;
 
@@ -41,11 +41,11 @@ export {
 	##
 	## version_string: Zeek version string.
 	##
-	## Returns: `VersionDescription` record.
+	## Returns: :zeek:see:`Version::VersionDescription` record.
 	global parse: function(version_string: string): VersionDescription;
 
-	## Test if the current running version of Zeek is greater or equal to the given version
-	## string.
+	## Test if the current running version of Zeek is greater or equal to
+	## the given version string.
 	##
 	## version_string: Version to check against the current running version.
 	##
@@ -118,13 +118,15 @@ function parse(version_string: string): VersionDescription
 	}
 
 export {
-	## `VersionDescription` record pertaining to the currently running version of Zeek.
+	## :zeek:see:`Version::VersionDescription` record pertaining to the currently
+	## running version of Zeek.
 	const info = Version::parse(zeek_version());
 
-	## version number of the currently running version of Zeek as a numeric representation.
-	## The format of the number is ABBCC with A being the major version,
-	## bb being the minor version (2 digits) and CC being the patchlevel (2 digits).
-	## As an example, Zeek 2.4.1 results in the number 20401
+	## version number of the currently running version of Zeek as a numeric
+	## representation.  The format of the number is ABBCC with A being the
+	## major version, bb being the minor version (2 digits) and CC being the
+	## patchlevel (2 digits).  As an example, Zeek 2.4.1 results in the
+	## number 20401
 	const number = info$version_number;
 }
 
diff --git a/scripts/base/utils/exec.zeek b/scripts/base/utils/exec.zeek
index 7f87bb7bb4..1fa7743325 100644
--- a/scripts/base/utils/exec.zeek
+++ b/scripts/base/utils/exec.zeek
@@ -6,7 +6,7 @@ module Exec;
 
 export {
 	type Command: record {
-		## The command line to execute.  Use care to avoid injection
+		## The command line to execute. Use care to avoid injection
 		## attacks (i.e., if the command uses untrusted/variable data,
 		## sanitize it with :zeek:see:`safe_shell_quote`).
 		cmd:         string;
@@ -34,10 +34,10 @@ export {
 	};
 
 	## Function for running command line programs and getting
-	## output.  This is an asynchronous function which is meant
-	## to be run with the `when` statement.
+	## output. This is an asynchronous function which is meant
+	## to be run with the ``when`` statement.
 	##
-	## cmd: The command to run.  Use care to avoid injection attacks!
+	## cmd: The command to run. Use care to avoid injection attacks!
 	##
 	## Returns: A record representing the full results from the
 	##          external program execution.
diff --git a/scripts/base/utils/numbers.zeek b/scripts/base/utils/numbers.zeek
index 41b8e601bb..114757f888 100644
--- a/scripts/base/utils/numbers.zeek
+++ b/scripts/base/utils/numbers.zeek
@@ -2,9 +2,9 @@
 ##
 ## s: The string to search for a number.
 ##
-## get_first: Provide `F` if you would like the last number found.
+## get_first: Provide ``F`` if you would like the last number found.
 ##
-## Returns: The request integer from the given string or 0 if
+## Returns: The request integer from the given string or ``0`` if
 ##          no integer was found.
 function extract_count(s: string, get_first: bool &default=T): count
 	{
diff --git a/scripts/policy/frameworks/packet-filter/shunt.zeek b/scripts/policy/frameworks/packet-filter/shunt.zeek
index 8fd2596fdc..86c162da3f 100644
--- a/scripts/policy/frameworks/packet-filter/shunt.zeek
+++ b/scripts/policy/frameworks/packet-filter/shunt.zeek
@@ -8,19 +8,19 @@ export {
 	const max_bpf_shunts = 100 &redef;
 
 	## Call this function to use BPF to shunt a connection (to prevent the
-	## data packets from reaching Zeek).  For TCP connections, control
+	## data packets from reaching Zeek). For TCP connections, control
 	## packets are still allowed through so that Zeek can continue logging
 	## the connection and it can stop shunting once the connection ends.
 	global shunt_conn: function(id: conn_id): bool;
 
 	## This function will use a BPF expression to shunt traffic between
-	## the two hosts given in the `conn_id` so that the traffic is never
+	## the two hosts given in the ``conn_id`` so that the traffic is never
 	## exposed to Zeek's traffic processing.
 	global shunt_host_pair: function(id: conn_id): bool;
 
-	## Remove shunting for a host pair given as a `conn_id`.  The filter
+	## Remove shunting for a host pair given as a ``conn_id``.  The filter
 	## is not immediately removed.  It waits for the occasional filter
-	## update done by the `PacketFilter` framework.
+	## update done by the ``PacketFilter`` framework.
 	global unshunt_host_pair: function(id: conn_id): bool;
 
 	## Performs the same function as the :zeek:id:`PacketFilter::unshunt_host_pair`
@@ -40,7 +40,7 @@ export {
 		No_More_Conn_Shunts_Available,
 
 		## Limitations in BPF make shunting some connections with BPF
-		## impossible.  This notice encompasses those various cases.
+		## impossible. This notice encompasses those various cases.
 		Cannot_BPF_Shunt_Conn,
 	};
 }
diff --git a/scripts/policy/frameworks/telemetry/log.zeek b/scripts/policy/frameworks/telemetry/log.zeek
index 8ee376eee4..a360a7ed4f 100644
--- a/scripts/policy/frameworks/telemetry/log.zeek
+++ b/scripts/policy/frameworks/telemetry/log.zeek
@@ -1,5 +1,5 @@
-##! Implementation of a telemetry.log and telemetry_histogram.log file
-##! using metrics accessible via the Telemetry module.
+##! Implementation of a :file:`telemetry.log` and :file:`telemetry_histogram.log`
+##! file using metrics accessible via the Telemetry module.
 
 @load base/frameworks/telemetry
 
@@ -12,8 +12,9 @@ export {
 	option log_interval = 60sec;
 
 	## Only metrics with prefixes in this set will be included in the
-	## `telemetry.log` and `telemetry_histogram.log` files by default.
-	## Setting this option to an empty set includes all prefixes.
+	## :file:`telemetry.log` and :file:`telemetry_histogram.log` files
+	## by default. Setting this option to an empty set includes all
+	## prefixes.
 	##
 	## For more fine-grained customization, setting this option to an
 	## empty set and implementing the :zeek:see:`Telemetry::log_policy`
diff --git a/src/event.bif b/src/event.bif
index e45c9c76a9..f89b099fa1 100644
--- a/src/event.bif
+++ b/src/event.bif
@@ -724,8 +724,8 @@ event file_over_new_connection%(f: fa_file, c: connection, is_orig: bool%);
 ## of the file.  The analysis can be augmented at this time via
 ## :zeek:see:`Files::add_analyzer`.  The amount of data fed into the file
 ## sniffing can be increased or decreased by changing either
-## :zeek:see:`default_file_bof_buffer_size` or the `bof_buffer_size` field
-## in an `fa_file` record. The event will be raised even if content inspection
+## :zeek:see:`default_file_bof_buffer_size` or the ``bof_buffer_size`` field
+## in an :zeek:type:`fa_file` record. The event will be raised even if content inspection
 ## has been unable to infer any metadata, in which case the fields in *meta*
 ## will be left all unset.
 ##
diff --git a/src/packet_analysis/packet_analysis.bif b/src/packet_analysis/packet_analysis.bif
index c90e2665c9..77766d1185 100644
--- a/src/packet_analysis/packet_analysis.bif
+++ b/src/packet_analysis/packet_analysis.bif
@@ -28,7 +28,7 @@ function register_packet_analyzer%(parent: PacketAnalyzer::Tag, identifier: coun
 	return zeek::val_mgr->True();
 	%}
 
-## Attempts to add an entry to `parent`'s dispatcher that maps a protocol/index to a next-stage `child`
+## Attempts to add an entry to ``parent``'s dispatcher that maps a protocol/index to a next-stage ``child``
 ## analyzer. This may fail if either of the two names does not respond to a known analyzer.
 ##
 ## parent: The parent analyzer being modified
@@ -49,7 +49,7 @@ function try_register_packet_analyzer_by_name%(parent: string, identifier: count
 	return zeek::val_mgr->True();
 	%}
 
-## Internal function that is used to update the core-mirror of the script-level `ignore_checksums_nets` variable.
+## Internal function that is used to update the core-mirror of the script-level ``ignore_checksums_nets`` variable.
 function PacketAnalyzer::__set_ignore_checksums_nets%(v: subnet_set%) : bool
 	%{
 	if ( v->GetType()->Tag() != zeek::TYPE_TABLE )