diff --git a/scripts/base/frameworks/file-analysis/main.bro b/scripts/base/frameworks/file-analysis/main.bro
index 772bb35159..0fbffcef9f 100644
--- a/scripts/base/frameworks/file-analysis/main.bro
+++ b/scripts/base/frameworks/file-analysis/main.bro
@@ -1,8 +1,7 @@
-##! TODO add some comments here
+##! An interface for driving the analysis of files, possibly independent of
+##! any network protocol over which they're transported.
 
 @load base/file_analysis.bif
-
-# TODO: do logging here?
 @load base/frameworks/logging
 
 module FileAnalysis;
@@ -13,10 +12,6 @@ export {
 		LOG
 	};
 
-	## The default buffer size used to reassemble files.
-	# TODO: what's a reasonable default?
-	const default_reassembly_buffer_size: count = 1024*1024 &redef;
-
 	## The default buffer size used for storing the beginning of files.
 	const default_bof_buffer_size: count = 1024 &redef;
 
@@ -24,29 +19,32 @@ export {
 	## before giving up.
 	const default_timeout_interval: interval = 2 mins &redef;
 
-	# Needed a forward declaration for event parameters...
-	type Info: record {};
-
+	## A structure which represents a desired file analysis action to take.
 	type ActionArgs: record {
+		## The type of action.
 		act: Action;
+		## The local filename to which to write an extracted file.  Must be
+		## set when *act* is :bro:see:`FileAnalysis::ACTION_EXTRACT`.
 		extract_filename: string &optional;
-		chunk_event: event(info: Info, data: string, off: count) &optional;
-		stream_event: event(info: Info, data: string) &optional;
 	};
 
+	## A structure which contains the results of certain file analysis actions.
 	type ActionResults: record {
+		## An MD5 digest of the file contents.
 		md5: string &optional;
+		## An SHA1 digest of the file contents.
 		sha1: string &optional;
+		## An SHA256 digest of the file contents.
 		sha256: string &optional;
 	};
 
-	## Contains all metadata related to the analysis of a given file, some
-	## of which is logged.
+	## Contains all metadata related to the analysis of a given file.
 	type Info: record {
-		## Unique identifier associated with a single file.
+		## An identifier associated with a single file.
 		file_id: string &log;
-		## Unique identifier associated with the file if it was extracted
-		## from a container file as part of the analysis.
+
+		## Identifier associated with a container file from which this one was
+		## extracted as part of the file analysis.
 		parent_file_id: string &log &optional;
 
 		## An identification of the source of the file data.  E.g. it may be
@@ -62,18 +60,17 @@ export {
 
 		## Number of bytes provided to the file analysis engine for the file.
 		seen_bytes: count &log &default=0;
-		## Total number of bytes that are supposed to comprise the file content.
+
+		## Total number of bytes that are supposed to comprise the full file.
 		total_bytes: count &log &optional;
 
 		## The number of bytes in the file stream that were completely missed
 		## during the process of analysis e.g. due to dropped packets.
-		## analysis that had to be discarded due to a reassembly buffer size
-		## of *reassembly_buffer_size* being filled.
 		missing_bytes: count &log &default=0;
 
 		## The number of not all-in-sequence bytes in the file stream that
 		## were delivered to file actions/analyzers due to reassembly buffer
-		## size of *reassembly_buffer_size* being filled.
+		## overflow.
 		overflow_bytes: count &log &default=0;
 
 		## The amount of time between receiving new data for this file that
@@ -81,60 +78,237 @@ export {
 		timeout_interval: interval &log &default=default_timeout_interval;
 
 		## The number of bytes at the beginning of a file to save for later
-		## inspection in *bof_buffer* field of
-		## :bro:see:`FileAnalysis::ActionResults`.
+		## inspection in *bof_buffer* field.
 		bof_buffer_size: count &log &default=default_bof_buffer_size;
 
 		## The content of the beginning of a file up to *bof_buffer_size* bytes.
 		## This is also the buffer that's used for file/mime type detection.
 		bof_buffer: string &optional;
 
-		## An initial guess at file type.
+		## A file type provided by libmagic against the *bof_buffer*, or
+		## in the cases where no buffering of the beginning of file occurs,
+		## an initial guess of the file type based on the first data seen.
 		file_type: string &log &optional;
-		## An initial guess at mime type.
+
+		## A mime type provided by libmagic against the *bof_buffer*, or
+		## in the cases where no buffering of the beginning of file occurs,
+		## an initial guess of the mime type based on the first data seen.
 		mime_type: string &log &optional;
 
 		## Actions that have been added to the analysis of this file.
-		## Not meant to be modified directly by scripts.
+		## Only meant for inspection by user scripts, not direct modification.
 		actions: table[ActionArgs] of ActionResults;
 	} &redef;
 
-	## TODO: document
+	## Fields that are derived from existing ones, and are set just in time
+	## for logging purposes.
+	redef record FileAnalysis::Info += {
+		## Whether the file analysis timed out at least once for the file.
+		timedout: bool &log &default=F;
+
+		## Connection UIDS over which the file was transferred.
+		conn_uids: set[string] &log &optional;
+
+		## A set of action types taken during the file analysis.
+		actions_taken: set[Action] &log &optional;
+
+		## Local filenames of file extraction actions.
+		extracted_files: set[string] &log &optional;
+
+		## An MD5 digest of the file contents.
+		md5: string &log &optional;
+
+		## A SHA1 digest of the file contents.
+		sha1: string &log &optional;
+
+		## A SHA256 digest of the file contents.
+		sha256: string &log &optional;
+	};
+
+	## Redefined here just so the *info* parameters of the events have the
+	## right type information.
+	redef record ActionArgs += {
+		## An event which will be generated for all new file contents,
+		## chunk-wise.
+		chunk_event: event(info: Info, data: string, off: count) &optional;
+
+		## An event which will be generated for all new file contents,
+		## stream-wise.
+		stream_event: event(info: Info, data: string) &optional;
+	};
+
+	## Evaluated every time a significant event occurs during the course of
+	## file analysis.  Fields of the *info* argument may be modified or
+	## other actions may be added or removed inside the body of any handlers
+	## of this hook.
 	global policy: hook(trig: Trigger, info: Info);
 
+	## A table that can be used to disable file analysis completely for
+	## any files transferred over given network protocol analyzers.
 	const disable: table[AnalyzerTag] of bool = table() &redef;
 
-	# TODO: wrapper functions for BiFs ?
-
 	## Event that can be handled to access the Info record as it is sent on
 	## to the logging framework.
 	global log_file_analysis: event(rec: Info);
 
 	## The salt concatenated to unique file handle strings generated by
-	## :bro:see:`FileAnalysis::handle_callbacks` before hashing them
-	## in to a file id (the *file_id* field of :bro:see:`FileAnalysis::Info`).
+	## :bro:see:`get_file_handle` before hashing them in to a file id
+	## (the *file_id* field of :bro:see:`FileAnalysis::Info`).
 	## Provided to help mitigate the possiblility of manipulating parts of
 	## network connections that factor in to the file handle in order to
 	## generate two handles that would hash to the same file id.
 	const salt = "I recommend changing this." &redef;
+
+	## Postpones the timeout of file analysis for a given file.
+	## When used within a :bro:see:`FileAnalysis::policy` handler for
+	## :bro:see:`FileAnalysis::TRIGGER_TIMEOUT`, the analysis will delay
+	## timing out for the period of time indicated by the *timeout_interval*
+	## field of :bro:see:`FileAnalysis::Info`.
+	##
+	## file_id: the file identifier string from the *file_id* field of
+	##          :bro:see:`FileAnalysis::Info`.
+	##
+	## Returns: true if the timeout will be postponed, or false if analysis
+	##          for the *file_id* isn't currently active.
+	global postpone_timeout: function(file_id: string): bool;
+
+	## Adds an action to the analysis of a given file.
+	##
+	## file_id: the file identifier string from the *file_id* field of
+	##          :bro:see:`FileAnalysis::Info`.
+	##
+	## args: the action type to add along with any arguments it takes.
+	##
+	## Returns: true if the action will be added, or false if analysis
+	##          for the *file_id* isn't currently active or the *args*
+	##          were invalid for the action type.
+	global add_action: function(file_id: string, args: ActionArgs): bool;
+
+	## Removes an action from the analysis of a given file.
+	##
+	## file_id: the file identifier string from the *file_id* field of
+	##          :bro:see:`FileAnalysis::Info`.
+	##
+	## args: the action (type and args) to remove.
+	##
+	## Returns: true if the action will be removed, or false if analysis
+	##          for the *file_id* isn't currently active.
+	global remove_action: function(file_id: string, args: ActionArgs): bool;
+
+	## Stops/ignores any further analysis of a given file.
+	##
+	## file_id: the file identifier string from the *file_id* field of
+	##          :bro:see:`FileAnalysis::Info`.
+	##
+	## Returns: true if analysis for the given file will be ignored for the
+	##          rest of it's contents, or false if analysis for the *file_id*
+	##          isn't currently active.
+	global stop: function(file_id: string): bool;
+
+	## Sends a sequential stream of data in for file analysis.
+	## Meant for use when providing external file analysis input (e.g.
+	## from the input framework).
+	##
+	## source: a string that uniquely identifies the logical file that the
+	##         data is a part of and describes its source.
+	##
+	## data: bytestring contents of the file to analyze.
+	global data_stream: function(source: string, data: string);
+
+	## Sends a non-sequential chunk of data in for file analysis.
+	## Meant for use when providing external file analysis input (e.g.
+	## from the input framework).
+	##
+	## source: a string that uniquely identifies the logical file that the
+	##         data is a part of and describes its source.
+	##
+	## data: bytestring contents of the file to analyze.
+	##
+	## offset: the offset within the file that this chunk starts.
+	global data_chunk: function(source: string, data: string, offset: count);
+
+	## Signals a content gap in the file bytestream.
+	## Meant for use when providing external file analysis input (e.g.
+	## from the input framework).
+	##
+	## source: a string that uniquely identifies the logical file that the
+	##         data is a part of and describes its source.
+	##
+	## offset: the offset within the file that this gap starts.
+	##
+	## len: the number of bytes that are missing.
+	global gap: function(source: string, offset: count, len: count);
+
+	## Signals the total size of a file.
+	## Meant for use when providing external file analysis input (e.g.
+	## from the input framework).
+	##
+	## source: a string that uniquely identifies the logical file that the
+	##         data is a part of and describes its source.
+	##
+	## size: the number of bytes that comprise the full file.
+	global set_size: function(source: string, size: count);
+
+	## Signals the end of a file.
+	## Meant for use when providing external file analysis input (e.g.
+	## from the input framework).
+	##
+	## source: a string that uniquely identifies the logical file that the
+	##         data is a part of and describes its source.
+	global eof: function(source: string);
 }
 
+function postpone_timeout(file_id: string): bool
+	{
+	return __postpone_timeout(file_id);
+	}
+
+function add_action(file_id: string, args: ActionArgs): bool
+	{
+	return __add_action(file_id, args);
+	}
+
+function remove_action(file_id: string, args: ActionArgs): bool
+	{
+	return __remove_action(file_id, args);
+	}
+
+function stop(file_id: string): bool
+	{
+	return __stop(file_id);
+	}
+
+function data_stream(source: string, data: string)
+	{
+	__data_stream(source, data);
+	}
+
+function data_chunk(source: string, data: string, offset: count)
+	{
+	__data_chunk(source, data, offset);
+	}
+
+function gap(source: string, offset: count, len: count)
+	{
+	__gap(source, offset, len);
+	}
+
+function set_size(source: string, size: count)
+	{
+	__set_size(source, size);
+	}
+
+function eof(source: string)
+	{
+	__eof(source);
+	}
+
 event bro_init() &priority=5
 	{
 	Log::create_stream(FileAnalysis::LOG,
 	                   [$columns=Info, $ev=log_file_analysis]);
 	}
 
-redef record FileAnalysis::Info += {
-	timedout: bool &log &default=F;
-	conn_uids: set[string] &log &optional;
-	actions_taken: set[Action] &log &optional;
-	extracted_files: set[string] &log &optional;
-	md5: string &log &optional;
-	sha1: string &log &optional;
-	sha256: string &log &optional;
-};
-
 hook FileAnalysis::policy(trig: FileAnalysis::Trigger, info: FileAnalysis::Info)
 	&priority=5
 	{
diff --git a/src/file_analysis.bif b/src/file_analysis.bif
index e00c1c8d05..826089bdbb 100644
--- a/src/file_analysis.bif
+++ b/src/file_analysis.bif
@@ -10,21 +10,23 @@ type Info: record;
 type ActionArgs: record;
 type ActionResults: record;
 
-## An enumeration of possibly-interesting "events" that can occur over
-## the course of analyzing files.  The :bro:see:`FileAnalysis::policy`
-## hook is called each time a trigger occurs.
+## An enumeration of significant things that can occur over the course of
+## analyzing files.  The :bro:see:`FileAnalysis::policy` hook is called each
+## time a trigger occurs.
 enum Trigger %{
+
 	## Raised when any part of a new file is detected.
 	TRIGGER_NEW,
+
 	## Raised when file is detected being transported over a new network
 	## connection (other than the first).
 	TRIGGER_NEW_CONN,
+
 	## Raised when file analysis has likely seen a complete file.  That
 	## is when a number of bytes indicated by the *total_bytes* field of
-	## :bro:see:`FileAnalysis::Info` have been processed.  Note that
-	## the *undelivered* field does not have to be zero for this to have
-	## occurred.
+	## :bro:see:`FileAnalysis::Info` have been processed.
 	TRIGGER_DONE,
+
 	## Raised when file analysis for a given file is aborted due
 	## to not seeing any data for it recently.  Note that this doesn't
 	## necessarily mean the full file wasn't seen (e.g. if the
@@ -33,44 +35,55 @@ enum Trigger %{
 	## during a :bro:see:`FileAnalysis::policy` handler for this trigger to
 	## defer the timeout until later.
 	TRIGGER_TIMEOUT,
+
 	## Raised when the beginning of a file is detected.
 	TRIGGER_BOF,
-	## Raised when the beginning of a file is available and that beginning
-	## is at least the number of bytes indicated by the *bof_buffer_size*
-	## field of :bro:see:`FileAnalysis::Info`.
+
+	## Raised when the beginning of a file is available in the *bof_buffer*
+	## field of :bro:see:`FileAnalysis::Info` and that beginning
+	## is at least the number of bytes indicated by the *bof_buffer_size* field.
 	TRIGGER_BOF_BUFFER,
-	## Raised when an initial guess at the file/mime type of a file is matched
-	## based on magic numbers.
+
+	## Raised when an initial guess at the file/mime type of a file is matched.
 	TRIGGER_TYPE,
+
 	## Raised to signal that no more file data is incoming and it couldn't be
-	## determined whether the full file was actually seen.
+	## determined whether the full file was actually seen and analyzed.
 	TRIGGER_EOF,
-	## The reassembly buffer for the file filled and had to be discarded.
-	## The *undelivered* field of :bro:see:`FileAnalysis::Info` will
-	## indicate the number of bytes, if any, that were not all-in-sequence.
-	## TODO: Is it possible to extend the reassembly buffer when "handling"
-	## this trigger?
-	TRIGGER_REASSEMBLY_BUFFER_FULL,
+
 	## Raised when there's a missing chunk of data in the file stream.
 	TRIGGER_GAP,
 %}
 
+## An enumeration of various file analysis actions that can be taken.
 enum Action %{
+
+	## Extract a file to local filesystem
 	ACTION_EXTRACT,
+
+	## Calculate an MD5 digest of the file's contents.
 	ACTION_MD5,
+
+	## Calculate an SHA1 digest of the file's contents.
 	ACTION_SHA1,
+
+	## Calculate an SHA256 digest of the file's contents.
 	ACTION_SHA256,
+
+	## Deliver the file contents to the script-layer in an event.
 	ACTION_DATA_EVENT,
 %}
 
-function FileAnalysis::postpone_timeout%(file_id: string%): bool
+## :bro:see:`FileAnalysis::postpone_timeout`.
+function FileAnalysis::__postpone_timeout%(file_id: string%): bool
 	%{
 	using file_analysis::FileID;
 	bool result = file_mgr->PostponeTimeout(FileID(file_id->CheckString()));
 	return new Val(result, TYPE_BOOL);
 	%}
 
-function FileAnalysis::add_action%(file_id: string, args: any%): bool
+## :bro:see:`FileAnalysis::add_action`.
+function FileAnalysis::__add_action%(file_id: string, args: any%): bool
 	%{
 	using file_analysis::FileID;
 	using BifType::Record::FileAnalysis::ActionArgs;
@@ -80,7 +93,8 @@ function FileAnalysis::add_action%(file_id: string, args: any%): bool
 	return new Val(result, TYPE_BOOL);
 	%}
 
-function FileAnalysis::remove_action%(file_id: string, args: any%): bool
+## :bro:see:`FileAnalysis::remove_action`.
+function FileAnalysis::__remove_action%(file_id: string, args: any%): bool
 	%{
 	using file_analysis::FileID;
 	using BifType::Record::FileAnalysis::ActionArgs;
@@ -90,39 +104,45 @@ function FileAnalysis::remove_action%(file_id: string, args: any%): bool
 	return new Val(result, TYPE_BOOL);
 	%}
 
-function FileAnalysis::stop%(file_id: string%): bool
+## :bro:see:`FileAnalysis::stop`.
+function FileAnalysis::__stop%(file_id: string%): bool
 	%{
 	using file_analysis::FileID;
 	bool result = file_mgr->IgnoreFile(FileID(file_id->CheckString()));
 	return new Val(result, TYPE_BOOL);
 	%}
 
-function FileAnalysis::data_stream%(source: string, data: string%): any
+## :bro:see:`FileAnalysis::data_stream`.
+function FileAnalysis::__data_stream%(source: string, data: string%): any
 	%{
 	file_mgr->DataIn(data->Bytes(), data->Len(), source->CheckString());
 	return 0;
 	%}
 
-function FileAnalysis::data_chunk%(source: string, data: string,
-                                         offset: count%): any
+## :bro:see:`FileAnalysis::data_chunk`.
+function FileAnalysis::__data_chunk%(source: string, data: string,
+                                     offset: count%): any
 	%{
 	file_mgr->DataIn(data->Bytes(), data->Len(), offset, source->CheckString());
 	return 0;
 	%}
 
-function FileAnalysis::gap%(source: string, offset: count, len: count%): any
+## :bro:see:`FileAnalysis::gap`.
+function FileAnalysis::__gap%(source: string, offset: count, len: count%): any
 	%{
 	file_mgr->Gap(offset, len, source->CheckString());
 	return 0;
 	%}
 
-function FileAnalysis::set_size%(source: string, size: count%): any
+## :bro:see:`FileAnalysis::set_size`.
+function FileAnalysis::__set_size%(source: string, size: count%): any
 	%{
 	file_mgr->SetSize(size, source->CheckString());
 	return 0;
 	%}
 
-function FileAnalysis::eof%(source: string%): any
+## :bro:see:`FileAnalysis::eof`.
+function FileAnalysis::__eof%(source: string%): any
 	%{
 	file_mgr->EndOfFile(source->CheckString());
 	return 0;
diff --git a/src/file_analysis/ActionSet.h b/src/file_analysis/ActionSet.h
index e1f1355aa9..aab3c1f94e 100644
--- a/src/file_analysis/ActionSet.h
+++ b/src/file_analysis/ActionSet.h
@@ -13,6 +13,11 @@ namespace file_analysis {
 class Info;
 declare(PDict,Action);
 
+/**
+ * A set of file analysis actions indexed by ActionArgs.  Allows queueing
+ * of addition/removals so that those modifications can happen at well-defined
+ * times (e.g. to make sure a loop iterator isn't invalidated).
+ */
 class ActionSet {
 public:
 
diff --git a/src/file_analysis/PendingFile.h b/src/file_analysis/PendingFile.h
index 58b842d969..678d7aff94 100644
--- a/src/file_analysis/PendingFile.h
+++ b/src/file_analysis/PendingFile.h
@@ -7,6 +7,10 @@
 
 namespace file_analysis {
 
+/**
+ * Provides buffering for file contents until the script-layer is able to
+ * return a unique file handle for it.
+ */
 class PendingFile {
 public:
 
diff --git a/testing/btest/Baseline/scripts.base.frameworks.file-analysis.logging/file_analysis.log b/testing/btest/Baseline/scripts.base.frameworks.file-analysis.logging/file_analysis.log
index 5d9322a8ae..482ac7216d 100644
--- a/testing/btest/Baseline/scripts.base.frameworks.file-analysis.logging/file_analysis.log
+++ b/testing/btest/Baseline/scripts.base.frameworks.file-analysis.logging/file_analysis.log
@@ -3,8 +3,8 @@
 #empty_field	(empty)
 #unset_field	-
 #path	file_analysis
-#open	2013-03-28-21-35-46
+#open	2013-03-29-18-28-57
 #fields	file_id	parent_file_id	source	last_active	seen_bytes	total_bytes	missing_bytes	overflow_bytes	timeout_interval	bof_buffer_size	file_type	mime_type	timedout	conn_uids	actions_taken	extracted_files	md5	sha1	sha256
 #types	string	string	string	time	count	count	count	count	interval	count	string	string	bool	table[string]	table[enum]	table[string]	string	string	string
-Cx92a0ym5R8	-	HTTP	1362692527.009775	4705	4705	0	0	120.000000	1024	set	set	F	UWkUyAuUGXf	FileAnalysis::ACTION_SHA1,FileAnalysis::ACTION_EXTRACT,FileAnalysis::ACTION_DATA_EVENT,FileAnalysis::ACTION_MD5,FileAnalysis::ACTION_SHA256	Cx92a0ym5R8-file	397168fd09991a0e712254df7bc639ac	1dd7ac0398df6cbc0696445a91ec681facf4dc47	4e7c7ef0984119447e743e3ec77e1de52713e345cde03fe7df753a35849bed18
-#close	2013-03-28-21-35-46
+Cx92a0ym5R8	-	HTTP	1362692527.009775	4705	4705	0	0	120.000000	1024	set	set	F	UWkUyAuUGXf	FileAnalysis::ACTION_SHA1,FileAnalysis::ACTION_DATA_EVENT,FileAnalysis::ACTION_EXTRACT,FileAnalysis::ACTION_MD5,FileAnalysis::ACTION_SHA256	Cx92a0ym5R8-file	397168fd09991a0e712254df7bc639ac	1dd7ac0398df6cbc0696445a91ec681facf4dc47	4e7c7ef0984119447e743e3ec77e1de52713e345cde03fe7df753a35849bed18
+#close	2013-03-29-18-28-57