diff --git a/LICENSE b/LICENSE
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+++ b/LICENSE
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+                    GNU AFFERO GENERAL PUBLIC LICENSE
+                       Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
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+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Affero General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Affero General Public License for more details.
+
+    You should have received a copy of the GNU Affero General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source.  For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code.  There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.
diff --git a/Setup.hs b/Setup.hs
new file mode 100644
--- /dev/null
+++ b/Setup.hs
@@ -0,0 +1,19 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import Distribution.Simple
+main = defaultMain
diff --git a/khph.cabal b/khph.cabal
new file mode 100644
--- /dev/null
+++ b/khph.cabal
@@ -0,0 +1,57 @@
+name: khph
+version: 0.1.0
+synopsis: Command-line file tagging and organization tool
+homepage: http://khumba.net/projects/khph
+license: AGPL-3
+license-file: LICENSE
+author: Bryan Gardiner <bog@khumba.net>
+maintainer: Bryan Gardiner <bog@khumba.net>
+copyright: Bryan Gardiner <bog@khumba.net>
+category: System
+build-type: Simple
+cabal-version: >=1.10
+description:
+  Khph is a tool for managing collections of files from the command line.  It
+  allows you to tag files via symlinks, and query your collection with a simple
+  query language.
+
+bug-reports: https://gitlab.com/khumba/issues
+source-repository head
+  type: git
+  location: https://gitlab.com/khumba/khph.git
+
+executable khph
+  default-language: Haskell2010
+  ghc-options: -W -fwarn-incomplete-patterns -fwarn-unused-do-bind
+  hs-source-dirs: src
+  main-is: Main.hs
+  other-modules:
+      Khph.Args
+    , Khph.Config
+    , Khph.Project.Base
+    , Khph.Project.Impl
+    , Khph.Project.Monad
+    , Khph.Query.Base
+    , Khph.Query.Eval
+    , Khph.Query.Parse
+    , Khph.Util
+  default-extensions:
+      TypeFamilies
+  other-extensions:
+      CPP
+    , OverloadedStrings
+  build-depends:
+      aeson >=0.8 && <0.12
+    , base >=4.7 && <4.9
+    , bytestring >=0.10 && <0.11
+    , cmdargs >=0.10 && <0.11
+    , containers >=0.5 && <0.6
+    , directory >=1.2 && <1.3
+    , filepath >=1.3 && <1.5
+    , mtl >=2.1 && <2.3
+    , parsec >=3.1 && <3.2
+    , text >=1.1 && <1.3
+    , transformers >=0.3 && <0.5
+    , unix >=2.7 && <2.8
+    , unordered-containers >=0.2 && <0.3
+    , yaml >=0.8 && <0.9
diff --git a/src/Khph/Args.hs b/src/Khph/Args.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Args.hs
@@ -0,0 +1,247 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE CPP #-}
+
+-- | Command-line argument parsing.
+module Khph.Args (
+  description,
+  CommonArgs (..),
+  Request (..),
+  parseFlags,
+  ) where
+
+#if !MIN_VERSION_base(4,8,0)
+import Control.Applicative ((<$), (<*), (*>))
+#endif
+import Data.Functor.Identity (Identity)
+import Khph.Util
+import System.Console.CmdArgs.Explicit (
+  Flag,
+  HelpFormat,
+  Mode,
+  flagArg,
+  flagBool,
+  flagHelpFormat,
+  flagNone,
+  flagReq,
+  helpText,
+  mode,
+  processArgs,
+  )
+import System.Console.CmdArgs.Text (TextFormat, showText)
+import Text.Parsec ((<|>), (<?>), ParsecT, anyToken, choice, eof, many, parse, try)
+
+-- | A summary string describing khph.
+description :: String
+description = "Command-line file tagging and organization tool"
+
+data CommonArgs = CommonArgs
+  { caProject :: String
+  , caPrintSummaries :: Bool
+  , caPrintFileActions :: Bool
+  }
+
+data Request =
+    FileCount
+  | List {listQuery :: Maybe String}
+  | TagList {tagListSpec :: Maybe String}
+  | TagCreate {tags :: [String]}
+  | TagAdd {tags :: [String], files :: [FilePath]}
+  | TagRemove {tags :: [String], files :: [FilePath]}
+  | Realize {tag :: String, query :: String, tagsInName :: Bool}
+  | Help
+  deriving (Show)
+
+data Term = TermFlag String | TermValue String
+          deriving (Eq)
+
+instance Show Term where
+  show (TermFlag str) = str
+  show (TermValue str) = concat ["non-flag argument \"", str, "\""]
+
+data Flags = Flags
+  { fProject :: String
+  , fTerms :: [Term]
+  , fPrintSummaries :: Bool
+  , fPrintFileActions :: Bool
+  , fHelp :: Maybe (HelpFormat, TextFormat)
+  , fTagsInName :: Bool
+  } deriving (Show)
+
+defaultFlags = Flags
+  { fProject = ""
+  , fTerms = []
+  , fPrintSummaries = True
+  , fPrintFileActions = False
+  , fHelp = Nothing
+  , fTagsInName = False
+  }
+
+projectUpdater :: String -> Flags -> Either String Flags
+projectUpdater value flags = case fProject flags of
+  "" -> Right flags {fProject = value}
+  _ -> Left "--project flag specified multiple times."
+
+printSummariesUpdater :: Bool -> Flags -> Flags
+printSummariesUpdater value flags = flags {fPrintSummaries = value}
+
+printFileActionsUpdater :: Bool -> Flags -> Flags
+printFileActionsUpdater value flags = flags {fPrintFileActions = value}
+
+tagsInNameUpdater :: Bool -> Flags -> Flags
+tagsInNameUpdater value flags = flags {fTagsInName = value}
+
+-- | Creates a cmdargs 'Flag' that parses a no-argument @--flag@ with the given
+-- name into a 'Term' in 'fTerms'
+flagTerm :: String -> String -> Flag Flags
+flagTerm name help =
+  flagNone [name] (\flags -> flags {fTerms = TermFlag ('-':'-':name) : fTerms flags}) help
+
+parameters :: Mode Flags
+parameters =
+  mode "khph" defaultFlags
+  (unlines [ description
+           , "    ><>"
+           , "Exactly one command must be provided.  Command arguments indicate"
+           , "their syntax in their description.  Other arguments are optional."
+           , "    ><>"
+           , "ENTRY : /foo/bar    - Absolute, refers to <project>/foo/bar."
+           , "        foo/bar     - Absolute, refers to <project>/foo/bar."
+           , "        ./foo/bar   - Relative, refers to $PWD/foo/bar."
+           , "        foo         - By-name, refers to all entries named foo."
+           , "TAG : Same as ENTRY, except by-name results match tags instead."
+           , "QUERY : A predicate to apply to entries.  See README.md."
+           ])
+  (flagArg (\x f -> Right f {fTerms = TermValue x : fTerms f}) "COMMAND")
+  [ flagHelpFormat $ \helpFormat textFormat f -> f {fHelp = Just (helpFormat, textFormat)}
+  , flagReq ["p", "project"] projectUpdater "PATH" "The project root directory or project file."
+  , flagBool ["print-summaries"] printSummariesUpdater "Print out summaries of actions performed."
+  , flagBool ["print-file-actions"] printFileActionsUpdater "Print out individual file actions."
+  , flagBool ["tags-in-name"] tagsInNameUpdater "Include tags in --realize'd link names."
+  , flagTerm "list" $
+    concat [ "--list [QUERY]: Lists one hard link (else soft link) for each "
+           , "entry matching the query (defaults to matching all entries)."
+           ]
+  , flagTerm "tags" "--tags [TAG]: Lists all tags (matching the given tag specification)."
+  , flagTerm "tag-create" $
+    concat [ "--tag-create TAG...: Creates the named tags, if they don't exist.  "
+           , "TAG must not be by-name."
+           ]
+  , flagTerm "tag-add" "--tag-add TAG... --files ENTRY...: Adds tags to entries."
+  , flagTerm "tag-remove" "--tag-remove TAG... --files ENTRY...: Removes tags from entries."
+  , flagTerm "realize" $
+    concat [ "--realize TAG QUERY: Creates TAG, removes it from all entries, then "
+           , "assigns entries matching QUERY to it."
+           ]
+  , flagTerm "files" ""
+  ]
+
+postProcessFlags :: Flags -> Flags
+postProcessFlags flags = flags {fTerms = reverse $ fTerms flags}
+
+parseFlags :: IO (Either String (CommonArgs, Maybe Request))
+parseFlags = do
+  flags <- fmap postProcessFlags $ processArgs parameters
+  let commonArgs =
+        CommonArgs
+        { caProject = fProject flags
+        , caPrintSummaries = fPrintSummaries flags
+        , caPrintFileActions = fPrintFileActions flags
+        }
+  case fHelp flags of
+    Just (helpFormat, textFormat) -> do
+      printHelp helpFormat textFormat
+      return $ Right (commonArgs, Just Help)
+    Nothing -> case parse requestParser "command line arguments" $ fTerms flags of
+      Left err -> return $ Left $ show err
+      Right maybeRequest ->
+        let postprocessedRequest = case maybeRequest of
+              Just request@(Realize {}) ->
+                Just $ request {tagsInName = fTagsInName flags}
+              _ -> maybeRequest
+        in return $ Right (commonArgs, postprocessedRequest)
+  -- TODO Validate common args.
+
+  where printHelp helpFormat textFormat =
+          putStrLn $ showText textFormat $ helpText [] helpFormat parameters
+
+type TermParser = ParsecT [Term] () Identity
+
+valueParser :: TermParser String
+valueParser =
+  try (do t <- anyToken
+          case t of
+            TermValue str -> return str
+            _ -> fail "") <?>
+  "non-flag argument"
+
+requestParser :: TermParser (Maybe Request)
+requestParser =
+  Nothing <$ eof <|>
+  Just <$> choice [ listParser
+                  , tagListParser
+                  , tagCreateParser
+                  , tagAddParser
+                  , tagRemoveParser
+                  , realizeParser
+                  ]
+
+listParser :: TermParser Request
+listParser =
+  parserEq (TermFlag "--list") *>
+  (List {listQuery = Nothing} <$ eof <|>
+   do q <- valueParser <* eof
+      return List {listQuery = Just q})
+
+tagListParser :: TermParser Request
+tagListParser =
+  parserEq (TermFlag "--tags") *>
+  (TagList {tagListSpec = Nothing} <$ eof <|>
+   do spec <- valueParser <* eof
+      return TagList {tagListSpec = Just spec})
+
+tagCreateParser :: TermParser Request
+tagCreateParser = do
+  parserEq $ TermFlag "--tag-create"
+  tags <- many valueParser
+  return TagCreate {tags = tags}
+
+tagAddParser :: TermParser Request
+tagAddParser = do
+  parserEq $ TermFlag "--tag-add"
+  tags <- many valueParser
+  parserEq $ TermFlag "--files"
+  files <- many valueParser
+  eof
+  return TagAdd {tags = tags, files = files}
+
+tagRemoveParser :: TermParser Request
+tagRemoveParser = do
+  parserEq $ TermFlag "--tag-remove"
+  tags <- many valueParser
+  parserEq $ TermFlag "--files"
+  files <- many valueParser
+  eof
+  return TagRemove {tags = tags, files = files}
+
+realizeParser :: TermParser Request
+realizeParser = do
+  parserEq $ TermFlag "--realize"
+  tag <- valueParser
+  query <- valueParser
+  return Realize {tag = tag, query = query, tagsInName = False}
diff --git a/src/Khph/Config.hs b/src/Khph/Config.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Config.hs
@@ -0,0 +1,105 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE CPP, OverloadedStrings #-}
+
+-- | Project configuration data types and parser.
+module Khph.Config (
+  Config,
+  defaultConfig,
+  configSourceDirs,
+  configIgnoredPaths,
+  readProjectFile,
+  ) where
+
+#if !MIN_VERSION_base(4,8,0)
+import Control.Applicative ((<$>))
+#endif
+import Control.Monad (unless, when)
+import Data.Aeson.Types (typeMismatch)
+import qualified Data.HashMap.Strict as HashMap
+import qualified Data.Set as Set
+import Data.Set (Set)
+import Data.Text (Text)
+import Data.Yaml (
+  (.:?),
+  (.!=),
+  FromJSON (parseJSON),
+  Object,
+  ParseException (UnexpectedEvent, _received, _expected),
+  Parser,
+  Value (Object),
+  decodeFileEither,
+  )
+import Khph.Project.Base
+import Khph.Util
+import System.FilePath (isAbsolute)
+import Text.Libyaml (Event (EventDocumentStart, EventStreamEnd))
+
+data Config = Config
+  { configSourceDirs :: Set ProjectPath
+  , configIgnoredPaths :: [ProjectPath]
+  } deriving (Show)
+
+-- | Used when the config file is empty or absent.
+defaultConfig :: Config
+defaultConfig = Config Set.empty []
+
+instance FromJSON Config where
+  parseJSON (Object o) = do
+    [sourceDirsKey, ignoredPathsKey] <- expectKeys "Config" o ["sourceDirs", "ignore"]
+    sourceDirs <- map stripTrailingPathSeparators <$> o .:? sourceDirsKey .!= []
+    ignoredPaths <- map stripTrailingPathSeparators <$> o .:? ignoredPathsKey .!= []
+
+    let absoluteSourceDirs = filter isAbsolute sourceDirs
+    when (not $ null absoluteSourceDirs) $
+      fail $ concat
+      ["sourceDirs: Source directories must be relative paths (to the project root): ",
+       show absoluteSourceDirs]
+
+    let absoluteIgnoredPaths = filter isAbsolute ignoredPaths
+    when (not $ null absoluteIgnoredPaths) $
+      fail $ concat
+      ["ignore: Ignored paths must be relative paths (to the project root): ",
+       show absoluteIgnoredPaths]
+
+    return Config
+      { configSourceDirs = Set.fromList $ map toProjectPath sourceDirs
+      , configIgnoredPaths = map toProjectPath ignoredPaths
+      }
+
+  parseJSON value = typeMismatch "Config" value
+
+readProjectFile :: FilePath -> IO (Either String Config)
+readProjectFile path =
+  either checkError Right <$> decodeFileEither path
+  where checkError err =
+          let isEmptyFile = case err of
+                UnexpectedEvent {_received = r, _expected = e} ->
+                  r == Just EventStreamEnd && e == Just EventDocumentStart
+                _ -> False
+          in if isEmptyFile then Right defaultConfig else Left $ show err
+
+-- | Returns the given list of keys, but first checks that an object doesn't
+-- contain more keys than those in the list.  If it does, then the parse is
+-- failed with a message containing the extraneous keys.
+expectKeys :: String -> Object -> [Text] -> Parser [Text]
+expectKeys typeName o keys = do
+  let extraKeys = Set.fromList (HashMap.keys o) `Set.difference` Set.fromList keys
+  unless (Set.null extraKeys) $
+    fail $ typeName ++ " has unknown keys: " ++ show (Set.toList extraKeys)
+  return keys
diff --git a/src/Khph/Project/Base.hs b/src/Khph/Project/Base.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Project/Base.hs
@@ -0,0 +1,168 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE OverloadedStrings #-}
+
+-- | Core data types for a project.
+module Khph.Project.Base (
+  -- * Project paths
+  ProjectPath,
+  toProjectPath,
+  projectPathFromComponents,
+  projectPathToComponents,
+  projectPathToRelativePath,
+  projectPathAppend,
+  projectPathAppendComponents,
+  projectPathDropLastComponent,
+  projectPathIsPrefixOf,
+  -- * Tags
+  Tag,
+  toTag,
+  tagToProjectPath,
+  tagToComponents,
+  tagToRelativePath,
+  -- * Entry lookup
+  EntrySpec (..),
+  toEntrySpec,
+  ) where
+
+import Data.Function (on)
+import Data.List (intercalate, intersperse, isPrefixOf)
+import Khph.Util
+import System.FilePath (isPathSeparator, isRelative, pathSeparator)
+
+-- | A project path is a relative path from a project's root directory,
+-- normalized so that there are no @.@ or @..@ components.
+data ProjectPath = ProjectPath
+  { projectPathToComponents :: [String]
+    -- ^ Returns the individual path components.
+  } deriving (Eq, Ord)
+
+instance Show ProjectPath where
+  show x = concat $
+           "<ProjectPath " :
+           intersperse [pathSeparator] (projectPathToComponents x) ++
+           [">"]
+
+-- | Converts a project-relative 'FilePath' into a 'ProjectPath'.  Errors if
+-- given an absolute path.
+toProjectPath :: FilePath -> ProjectPath
+toProjectPath path =
+  if isRelative path
+  then projectPathFromComponents $ splitPath path
+  else error $ concat
+       ["toProjectPath: Expected a relative path, got ", show path, "."]
+
+-- | Creates a 'ProjectPath' from a list of path components.  Removes empty
+-- components.
+projectPathFromComponents :: [String] -> ProjectPath
+projectPathFromComponents =
+  ProjectPath . filter (not . null)  -- The filter here is defensive.
+
+-- | Converts a 'ProjectPath' to a 'FilePath' relative to the project root.
+projectPathToRelativePath :: ProjectPath -> FilePath
+projectPathToRelativePath projectPath =
+  case intercalate [pathSeparator] $ projectPathToComponents projectPath of
+    "" -> "."
+    path -> path
+
+-- | Appends the components from a 'FilePath' on to the end of a 'ProjectPath'.
+projectPathAppend :: ProjectPath -> FilePath -> ProjectPath
+projectPathAppend projectPath suffix =
+  projectPathAppendComponents projectPath $ splitPath suffix
+
+-- | Appends path components onto a 'ProjectPath'.
+projectPathAppendComponents :: ProjectPath -> [String] -> ProjectPath
+projectPathAppendComponents projectPath components =
+  projectPathFromComponents $
+  (++ components) $
+  projectPathToComponents projectPath
+
+-- | Drops the last component of a file path.
+projectPathDropLastComponent :: ProjectPath -> ProjectPath
+projectPathDropLastComponent (ProjectPath xs) = ProjectPath $ butLast xs
+
+-- | @projectPathIsPrefixOf p1 p2@ returns whether @p1@ is either equal to @p2@
+-- or is an ancestor of @p2@.
+projectPathIsPrefixOf :: ProjectPath -> ProjectPath -> Bool
+projectPathIsPrefixOf = isPrefixOf `on` projectPathToComponents
+
+-- | A tag is a link outside of all project source directories to a file inside
+-- a source directory.  Both the link and the file may be either hard or soft
+-- links.
+newtype Tag = Tag
+  { tagToProjectPath :: ProjectPath
+    -- ^ Returns the 'ProjectPath' underlying a 'Tag'.
+  } deriving (Eq, Ord)
+
+instance Show Tag where
+  show tag = concat ["<Tag ", tagToRelativePath tag, ">"]
+
+-- | You should probably use 'tagParse' instead of this function.
+toTag :: ProjectPath -> Either String Tag
+toTag projectPath@(ProjectPath components) = case components of
+  [] -> Left "toTag: An empty project path may not be a tag."
+  _ -> Right $ Tag projectPath
+
+-- | Shortcut for @'projectPathToComponents' . 'tagToProjectPath'@.
+tagToComponents :: Tag -> [String]
+tagToComponents = projectPathToComponents . tagToProjectPath
+
+-- | Shortcut for @'projectPathToRelativePath' . 'tagToProjectPath'@.
+tagToRelativePath :: Tag -> String
+tagToRelativePath = projectPathToRelativePath . tagToProjectPath
+
+-- | A textual, user-friendly pattern that matches zero or more entries in a
+-- project.  A 'EntrySpec' can be absolute, relative, or by-name.  Absolute
+-- 'EntrySpec's represent a single path from the root of the project to a
+-- possible entry.  Relative 'EntrySpec's represent a single path from the
+-- current working directory to a possible entry.  By-name 'EntrySpec's store
+-- only a single file name, and refer to all entries that have that name in
+-- their last component of some path.
+--
+-- The textual format for a 'EntrySpec' is as follows.  The string may not be
+-- empty.  Strings that begin with a path separator (see 'isPathSeparator') are
+-- absolute.  Strings that begin with @.@ then a path separator are relative.
+-- Otherwise, strings that contain a path separator are absolute and strings
+-- that do not are relative.  This may be relaxed in the future by making
+-- additional strings not starting with a path separator to be not absolute.
+data EntrySpec =
+    EntrySpecAbsolute [String]
+  | EntrySpecRelative [String]
+  | EntrySpecByName String
+  deriving (Eq)
+
+instance Show EntrySpec where
+  show spec = case spec of
+    EntrySpecAbsolute components ->
+      concat $ "<EntrySpec " : map (pathSeparator:) components ++ [">"]
+    EntrySpecRelative components ->
+      concat $ "<EntrySpec ." : map (pathSeparator:) components ++ [">"]
+    EntrySpecByName name ->
+      concat ["<EntrySpec ", name, ">"]
+
+-- | Parses an 'EntrySpec', returning an error message if the parse fails.
+toEntrySpec :: String -> Either String EntrySpec
+toEntrySpec str = case str of
+  [] -> Left "toEntrySpec: An empty entry specification is invalid."
+  c:[] | isPathSeparator c -> Right $ EntrySpecAbsolute []
+  c:rest | isPathSeparator c -> Right $ EntrySpecAbsolute $ splitPath rest
+  '.':[] -> Right $ EntrySpecRelative []
+  '.':c:rest | isPathSeparator c -> Right $ EntrySpecRelative $ splitPath rest
+  _ -> if any isPathSeparator str
+       then Right $ EntrySpecAbsolute $ splitPath str
+       else Right $ EntrySpecByName str
diff --git a/src/Khph/Project/Impl.hs b/src/Khph/Project/Impl.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Project/Impl.hs
@@ -0,0 +1,559 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE CPP #-}
+
+-- | Implementation of the project monad.
+module Khph.Project.Impl (Project, ProjectT, run) where
+
+#if !MIN_VERSION_base(4,8,0)
+import Control.Applicative ((<$>), (<*>), Applicative, pure)
+#endif
+import Control.Monad (ap, filterM, forM, forM_, liftM, unless, when)
+import Control.Monad.IO.Class (MonadIO, liftIO)
+import qualified Control.Monad.State as State
+import Control.Monad.State (StateT, evalStateT)
+import Control.Monad.Trans (MonadTrans, lift)
+import Data.Function (on)
+import Data.IORef (modifyIORef, newIORef, readIORef, writeIORef)
+import Data.List (intercalate, isSuffixOf, partition)
+import qualified Data.Map as Map
+import Data.Map (Map)
+import Data.Maybe (fromJust, fromMaybe, isNothing, listToMaybe)
+import qualified Data.Set as Set
+import Data.Set (Set)
+import Khph.Args (CommonArgs (..))
+import Khph.Config
+import Khph.Project.Base
+import Khph.Project.Monad
+import Khph.Query.Eval
+import Khph.Util
+import System.Directory (
+  canonicalizePath,
+  createDirectoryIfMissing,
+  doesFileExist,
+  getCurrentDirectory,
+  getDirectoryContents,
+  removeFile,
+  )
+import System.Exit (exitFailure)
+import System.FilePath ((</>), makeRelative, pathSeparator, takeFileName)
+import System.IO (hPutStrLn, stderr)
+import System.IO.Error (catchIOError, isDoesNotExistError)
+import System.Posix (
+  DeviceID,
+  FileID,
+  FileStatus,
+  createSymbolicLink,
+  deviceID,
+  fileID,
+  getFileStatus,
+  getSymbolicLinkStatus,
+  isDirectory,
+  isSymbolicLink,
+  )
+
+-- TODO This should be controllable.
+basicIgnoredSuffixes :: [String]
+basicIgnoredSuffixes = ["~"]
+
+data Project = Project
+  { projectRoot :: FilePath
+  , projectFileName :: Maybe FilePath
+  , projectConfig :: Config
+  , projectCommonArgs :: CommonArgs
+  , projectEntriesById :: Map EntryId EntryImpl
+  , projectEntriesByPath :: Map ProjectPath EntryId
+  , projectEntriesByTag :: Map Tag (Set EntryId)
+  , projectTags :: Set Tag
+  }
+
+data EntryImpl = EntryImpl
+  { entryImplId :: EntryId
+  , entryImplStat :: FileStatus
+  , entryImplHardLinks :: Set ProjectPath
+  , entryImplSoftLinks :: Set ProjectPath
+  , entryImplSourcePath :: Maybe ProjectPath
+  , entryImplTags :: Map Tag ProjectPath
+  }
+
+instance Eq EntryImpl where
+  (==) = (==) `on` entryImplId
+
+instance Ord EntryImpl where
+  compare = compare `on` entryImplId
+
+instance Show EntryImpl where
+  show entry =
+    let softLinksMsg = case Set.toList $ entryImplSoftLinks entry of
+          [] -> ">"
+          [x] -> concat ["; soft link ", projectPathToRelativePath x, ">"]
+          xs -> concat ["; ", show $ length xs, " soft links>"]
+
+    in case Set.toList $ entryImplHardLinks entry of
+      [] -> concat ["<Entry", softLinksMsg]
+      [x] -> concat ["<Entry ", projectPathToRelativePath x, softLinksMsg]
+      xs@(x:_) -> concat ["Entry ", projectPathToRelativePath x, "; ", show xs,
+                          " hard links", softLinksMsg]
+
+entryImplLinks :: EntryImpl -> [ProjectPath]
+entryImplLinks entry =
+  Set.toList (entryImplHardLinks entry) ++
+  Set.toList (entryImplSoftLinks entry)
+
+newtype EntryId = EntryId (DeviceID, FileID)
+                deriving (Eq, Ord, Show)
+
+data ProjectT m a = ProjectT { runProjectT' :: StateT Project m a }
+
+instance Monad m => Functor (ProjectT m) where
+  fmap = liftM
+
+instance Monad m => Applicative (ProjectT m) where
+  pure = return
+  (<*>) = ap
+
+instance Monad m => Monad (ProjectT m) where
+  return = ProjectT . return
+
+  (ProjectT x) >>= f = ProjectT $ runProjectT' . f =<< x
+
+instance MonadTrans ProjectT where
+  lift = ProjectT . lift
+
+instance MonadIO m => MonadIO (ProjectT m) where
+  liftIO = ProjectT . liftIO
+
+instance MonadIO m => MonadProject (ProjectT m) where
+  type Entry (ProjectT m) = EntryImpl
+
+  projectWarn msg = liftIO $ hPutStrLn stderr $ "khph: Warning: " ++ msg
+
+  projectDie msg = liftIO $ do
+    hPutStrLn stderr $ "khph: Error: " ++ msg
+    exitFailure
+
+  printSummary msg = do
+    proceed <- caPrintSummaries . projectCommonArgs <$> get
+    when proceed $ liftIO $ hPutStrLn stderr msg
+
+  printFileAction msg = do
+    proceed <- caPrintFileActions . projectCommonArgs <$> get
+    when proceed $ liftIO $ hPutStrLn stderr msg
+
+  getConfig = projectConfig <$> get
+
+  getCurrentPathOrDie reason = do
+    root <- projectRoot <$> get
+    dir <- liftIO $ canonicalizePath =<< getCurrentDirectory
+    if pathIsAncestor root dir
+      then return $ toProjectPath $ makeRelative root dir
+      else projectDie $ concat $
+           "getCurrentPath: Expected the current path " : show dir :
+            " to be below the project root " : show root :
+            if null reason then ["."] else [", ", reason, "."]
+
+  parseRealPath path = do
+    root <- projectRoot <$> get
+    liftIO $ parseRealPath' root path
+
+  pathRealize projectPath = do
+    root <- projectRoot <$> get
+    return $ pathRealize' root projectPath
+
+  entrySpecLookup entrySpec = case entrySpec of
+    EntrySpecAbsolute components -> return [projectPathFromComponents components]
+
+    EntrySpecRelative components -> do
+      currentPath <- getCurrentPathOrDie $ "looking for tags matching " ++ show entrySpec
+      return [projectPathAppendComponents currentPath components]
+
+    EntrySpecByName name ->
+      filter (\path -> maybeLast (projectPathToComponents path) == Just name) .
+      Map.keys .
+      projectEntriesByPath <$>
+      get
+
+  entryAtPath projectPath = do
+    project <- get
+    return $
+      flip Map.lookup (projectEntriesById project) =<<
+      flip Map.lookup (projectEntriesByPath project) projectPath
+
+  queryEntries query = filterM (queryApply query) . Map.elems . projectEntriesById =<< get
+
+  entryHardLinks = return . Set.toList . entryImplHardLinks
+
+  entrySoftLinks = return . Set.toList . entryImplSoftLinks
+
+  entrySourcePath = return . entryImplSourcePath
+
+  entryTags = return . Map.keys . entryImplTags
+
+  tagList = projectTags <$> get
+
+  -- TODO Reuse entrySpecLookup?
+  tagLookup entrySpec = case entrySpec of
+    EntrySpecAbsolute components -> case toTag $ projectPathFromComponents components of
+      Left err -> oops err
+      Right tag -> doLookup tag
+
+    EntrySpecRelative components -> do
+      currentPath <- getCurrentPathOrDie $ "looking for tags matching " ++ show entrySpec
+      case toTag $ projectPathAppendComponents currentPath components of
+        Left err -> oops err
+        Right tag -> doLookup tag
+
+    EntrySpecByName name ->
+      filter (\tag -> maybeLast (tagToComponents tag) == Just name) .
+      Set.toList <$>
+      tagList
+
+    where doLookup tag = do
+            found <- Set.member tag <$> tagList
+            return $ if found then [tag] else []
+
+          oops err =
+            projectDie $ concat
+            ["tagLookup: Failed to create tag object from ", show entrySpec, ": ", err]
+
+  tagCreate entrySpec = do
+    -- By-name EntrySpecs are not allowed for tag creation.
+    case entrySpec of
+      EntrySpecByName name ->
+        projectDie $ concat
+        ["tagCreate: By-name tag specifications are not allowed, ",
+         "please use an absolute or relative specification (",
+         pathSeparator:name, " or .", pathSeparator:name, ")."]
+      _ -> return ()
+
+    -- If the tag exists, we don't need to do anything.
+    existingTags <- tagLookup entrySpec
+    case existingTags of
+      [] -> do
+        -- The tag doesn't exist, let's create it!  Determine a project path for
+        -- the tag.  EntrySpecByName doesn't make any sense here, we need a
+        -- concrete path.
+        projectPath <- case entrySpec of
+          EntrySpecAbsolute components -> return $ projectPathFromComponents components
+          EntrySpecRelative components -> do
+            currentPath <- getCurrentPathOrDie $ "creating tag for " ++ show entrySpec
+            return $ projectPathAppendComponents currentPath components
+          EntrySpecByName _ ->
+            projectDie $ concat
+            ["tagCreate: Internal error, still have a by-name spec ", show entrySpec, "."]
+        -- Calculate a valid Tag object.
+        tag <- case toTag projectPath of
+          Left err ->
+            projectDie $ concat
+            ["tagCreate: Couldn't create tag object from ", show entrySpec, ": ", err]
+          Right tag -> return tag
+        -- Create the necessary directories.
+        path <- pathRealize projectPath
+        printFileAction $ concat ["mkdir -p ", path]
+        liftIO $ createDirectoryIfMissing True path
+        -- Update internal state.
+        modify $ \project -> project {projectTags = Set.insert tag $ projectTags project}
+        return (tag, True)
+      [tag] -> return (tag, False)  -- The tag already exists.
+      _ -> projectDie $ concat
+           ["tagCreate: Internal error, ", show entrySpec,
+            " matches multiple existing tags: ", show existingTags]
+
+  tagAdd entries tags = do
+    ensureSourcePathsExist entries
+    forM_ tags $ \tag -> tagAdd' tag $ map (\entry -> (entry, Nothing)) entries
+
+  tagAdd1 entry tag baseNameMaybe = do
+    ensureSourcePathsExist [entry]
+    tagAdd' tag [(entry, baseNameMaybe)]
+
+  tagRemove entries tags = do
+    ensureSourcePathsExist entries
+
+    forM_ tags $ \tag ->
+      forM_ entries $ \entry -> case Map.lookup tag $ entryImplTags entry of
+        Nothing -> return ()
+        Just projectPath -> do
+          path <- pathRealize projectPath
+          -- Sanity check: Ensure that this is a soft link.
+          lstat <- liftIO $ getSymbolicLinkStatus path
+          if isSymbolicLink lstat
+            then do -- Remove the tag on disk.
+                    printFileAction $ concat ["rm ", path]
+                    liftIO $ removeFile path
+
+                    -- Update the project in memory.
+                    let entry' = entry { entryImplSoftLinks = Set.delete projectPath $
+                                                              entryImplSoftLinks entry
+                                       , entryImplTags = Map.delete tag $ entryImplTags entry
+                                       }
+                        entryId = entryImplId entry'
+                    modify $ \project ->
+                      project { projectEntriesById = Map.insert entryId entry' $
+                                                     projectEntriesById project
+                              , projectEntriesByPath = Map.delete projectPath $
+                                                       projectEntriesByPath project
+                              , projectEntriesByTag = Map.adjust (Set.delete entryId) tag $
+                                                      projectEntriesByTag project
+                              }
+
+            else projectWarn $ concat
+                 ["tagRemove: Want to remove ", show tag, " from ", show projectPath,
+                  ", but the file is not a soft link.  Not removing."]
+
+get :: Monad m => ProjectT m Project
+get = ProjectT State.get
+
+modify :: Monad m => (Project -> Project) -> ProjectT m ()
+modify = ProjectT . State.modify
+
+-- | Ensures that we have at least one source path for all given entries.
+ensureSourcePathsExist :: MonadIO m => [EntryImpl] -> ProjectT m ()
+ensureSourcePathsExist entries =
+  case filter (isNothing . entryImplSourcePath) entries of
+    [] -> return ()
+    xs -> projectDie $ concat $
+          "tagAdd: The following entries aren't linked in source directories: " :
+          map (("\n- " ++) . show) xs
+
+run :: MonadIO m => CommonArgs -> FilePath -> Maybe FilePath -> ProjectT m a -> m a
+run commonArgs projectDir maybeProjectFile action = do
+  loaded <- load commonArgs projectDir maybeProjectFile
+  case loaded of
+    Left err -> die err
+    Right project -> evalStateT (runProjectT' action) project
+
+load :: MonadIO m => CommonArgs -> FilePath -> Maybe FilePath -> m (Either String Project)
+load commonArgs projectRootRaw maybeProjectFileName = do
+  projectRoot <- liftIO $ canonicalizePath projectRootRaw
+  let maybeProjectFilePath = (projectRoot </>) <$> maybeProjectFileName
+  configResult <- case maybeProjectFilePath of
+    Nothing -> return $ Right defaultConfig
+    Just projectFilePath -> do
+      projectFileExists <- liftIO $ doesFileExist projectFilePath
+      if projectFileExists
+        then liftIO $ readProjectFile projectFilePath
+        else return $ Right defaultConfig
+  case configResult of
+    Left err -> return $ Left $ "Error parsing project file: " ++ err
+    Right config -> do
+      let sourceDirs = Set.toList $ configSourceDirs config
+          basicIgnoredPaths = (maybe id (:) maybeProjectFilePath) [projectRoot]
+          customIgnoredPaths = Set.fromList $
+                               map (pathRealize' projectRoot) $
+                               configIgnoredPaths config
+
+      entriesByIdRef <- liftIO $ newIORef Map.empty
+      entriesByTagRef <- liftIO $ newIORef Map.empty
+      tagsRef <- liftIO $ newIORef Set.empty
+
+      forAllEntriesRecursively projectRoot $ \path -> do
+        let (process, recur) = case undefined of
+              _ | Set.member path customIgnoredPaths -> (False, False)
+              _ | elem path basicIgnoredPaths ||
+                  any (`isSuffixOf` path) basicIgnoredSuffixes -> (False, True)
+              _ -> (True, True)
+
+        when process $ do
+          maybeStat <- liftIO $ catchIOError (Just <$> getFileStatus path) $ \e ->
+            if isDoesNotExistError e
+            then return Nothing
+            else ioError e
+          lstat <- liftIO $ getSymbolicLinkStatus path
+
+          case maybeStat of
+            Nothing -> return ()  -- Dead soft link, ignore it.
+            Just stat -> case (isDirectory lstat, isDirectory stat) of
+              -- Ignore soft links to directories.
+              (False, True) -> return ()
+
+              (True, _) -> do
+                projectPath <- liftIO $
+                               either (\err ->
+                                        die $ concat
+                                        ["load: Couldn't parse a project path for ",
+                                         show path, ": ", err])
+                                      return =<<
+                               parseRealPath' projectRoot path
+                when (not (any (\src -> projectPathIsPrefixOf src projectPath) sourceDirs)) $ do
+                  tag <- either (\err ->
+                                  die $ concat ["load: Error parsing tag from directory ",
+                                                show path, ":", err])
+                                return $
+                         toTag projectPath
+                  liftIO $ do
+                    modifyIORef tagsRef $ Set.insert tag
+                    modifyIORef entriesByTagRef $ Map.insert tag Set.empty
+
+              (False, False) -> do
+                let entryId = EntryId (deviceID stat, fileID stat)
+                    projectPath = toProjectPath $ makeRelative projectRoot path
+
+                liftIO $ do
+                  entriesById <- readIORef entriesByIdRef
+
+                  let maybeEntry = Map.lookup entryId entriesById
+
+                      entryInitial =
+                        flip fromMaybe maybeEntry $
+                        EntryImpl
+                        { entryImplId = entryId
+                        , entryImplStat = stat
+                        , entryImplHardLinks = Set.empty
+                        , entryImplSoftLinks = Set.empty
+                        , entryImplSourcePath = Nothing
+                        , entryImplTags = Map.empty
+                        }
+
+                      entryWithLinks =
+                        if isSymbolicLink lstat
+                        then entryInitial
+                             { entryImplSoftLinks =
+                               Set.insert projectPath $ entryImplSoftLinks entryInitial
+                             }
+                        else entryInitial
+                             { entryImplHardLinks =
+                               Set.insert projectPath $ entryImplHardLinks entryInitial
+                             }
+
+                      isSourcePath path =
+                        any (\sourceDir -> projectPathIsPrefixOf sourceDir path) sourceDirs
+
+                      (sourcePaths, tagPaths) =
+                        partition isSourcePath $ entryImplLinks entryWithLinks
+
+                  -- If we have no source paths for a file, then ignore any tag
+                  -- (i.e. non-source) paths for the file, since it doesn't make
+                  -- sense to have a bunch of tags on a file we don't manage.
+                  entryWithTags <-
+                    if null sourcePaths
+                    then return entryWithLinks
+                    else do tags <- forM tagPaths $ \tagPath ->
+                              case toTag $ projectPathDropLastComponent tagPath of
+                                Left err ->
+                                  die $ concat ["load: Error parsing tag from path ",
+                                                show tagPath, ": ", err]
+                                Right tag -> return (tag, tagPath)
+                            return entryWithLinks
+                              { entryImplSourcePath = listToMaybe sourcePaths
+                              , entryImplTags = Map.fromList tags
+                              }
+
+                  -- Update entriesById.
+                  writeIORef entriesByIdRef $ Map.insert entryId entryWithTags entriesById
+                  -- Update entriesByTag.
+                  case Map.keys $ entryImplTags entryWithTags of
+                    [] -> return ()
+                    tags -> modifyIORef entriesByTagRef $ \entriesByTag ->
+                      foldr (\tag entriesByTag' ->
+                               Map.alter (Just . Set.insert entryId . fromMaybe Set.empty)
+                                         tag
+                                         entriesByTag')
+                            entriesByTag
+                            tags
+
+        return recur
+
+      entriesById <- liftIO $ readIORef entriesByIdRef
+      entriesByTag <- liftIO $ readIORef entriesByTagRef
+      tags <- liftIO $ readIORef tagsRef
+
+      let entries :: [EntryImpl]
+          entries = Map.elems entriesById
+
+          entriesByPath :: Map ProjectPath EntryId
+          entriesByPath = foldr (\entry m -> foldr (\path -> Map.insert path $ entryImplId entry)
+                                             m
+                                             (Set.toList (entryImplHardLinks entry) ++
+                                              Set.toList (entryImplSoftLinks entry)))
+                          Map.empty
+                          entries
+
+          project :: Project
+          project =
+            Project
+            { projectRoot = projectRoot
+            , projectFileName = maybeProjectFileName
+            , projectConfig = config
+            , projectCommonArgs = commonArgs
+            , projectEntriesById = entriesById
+            , projectEntriesByPath = entriesByPath
+            , projectEntriesByTag = entriesByTag
+            , projectTags = tags
+            }
+
+      return $ Right project
+
+parseRealPath' :: FilePath -> FilePath -> IO (Either String ProjectPath)
+parseRealPath' root path = do
+    canonicalPath <- canonicalizePath path
+    if pathIsAncestor root canonicalPath
+      then return $ Right $ toProjectPath $ makeRelative root canonicalPath
+      else return $ Left $ concat
+           ["parseRealPath: Path ", show canonicalPath,
+            " is not below the project root ", show root, "."]
+
+pathRealize' :: FilePath -> ProjectPath -> FilePath
+pathRealize' root path = root </> projectPathToRelativePath path
+
+tagAdd' :: MonadIO m => Tag -> [(EntryImpl, Maybe String)] -> ProjectT m ()
+tagAdd' tag entriesAndBaseNames = do
+  let tagComponents = tagToComponents tag
+      upToRoot = intercalate [pathSeparator] $ replicate (length tagComponents) ".."
+
+  forM_ entriesAndBaseNames $ \(entry, baseNameMaybe) ->
+    unless (Map.member tag $ entryImplTags entry) $ do
+      tagDir <- pathRealize $ tagToProjectPath tag
+      let entryPath = projectPathToRelativePath $ fromJust $ entryImplSourcePath entry
+          entryBaseName = takeFileName entryPath
+          linkSourcePath = tagDir </> fromMaybe entryBaseName baseNameMaybe
+          linkTargetPath = upToRoot </> entryPath
+
+      -- Add the tag on disk.
+      printFileAction $ concat ["ln -s ", linkTargetPath, " ", linkSourcePath]
+      liftIO $ createSymbolicLink linkTargetPath linkSourcePath
+
+      -- Update the project in memory.
+      let linkSourceProjectPath = projectPathAppend (tagToProjectPath tag) entryBaseName
+          entry' = entry { entryImplSoftLinks = Set.insert linkSourceProjectPath $
+                                                entryImplSoftLinks entry
+                         , entryImplTags = Map.insert tag linkSourceProjectPath $
+                                           entryImplTags entry
+                         }
+          entryId = entryImplId entry'
+      modify $ \project ->
+        project { projectEntriesById = Map.insert entryId entry' $
+                                       projectEntriesById project
+                , projectEntriesByPath = Map.insert linkSourceProjectPath entryId $
+                                         projectEntriesByPath project
+                , projectEntriesByTag =
+                  Map.alter (Just . Set.insert entryId . fromMaybe Set.empty) tag $
+                  projectEntriesByTag project
+                }
+
+forAllEntriesRecursively :: MonadIO m => FilePath -> (FilePath -> m Bool) -> m ()
+forAllEntriesRecursively root action = go root
+  where go path = do
+          recur <- action path
+          when recur $ do
+            typ <- liftIO $ getFileType path
+            when (typ == Directory) $ do
+              droppingIOErrors (getDirectoryContents path) $ \contents ->
+                forM_ contents $ \entry ->
+                unless (entry `elem` [".", ".."]) $
+                go $ path </> entry
diff --git a/src/Khph/Project/Monad.hs b/src/Khph/Project/Monad.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Project/Monad.hs
@@ -0,0 +1,177 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE CPP #-}
+
+-- | A monad for performing operations on a project.
+module Khph.Project.Monad (
+  MonadProject (..),
+  dumpProjectContents,
+  ) where
+
+#if !MIN_VERSION_base(4,8,0)
+import Control.Applicative (Applicative)
+#endif
+import Control.Monad (forM_)
+import Control.Monad.Trans (lift)
+import Control.Monad.IO.Class (MonadIO, liftIO)
+import Data.Set (Set)
+import Khph.Config (Config)
+import Khph.Project.Base
+import Khph.Query.Base
+import Text.Parsec (ParsecT)
+
+-- | A monad for performing operations on a project.
+class (Functor m, Applicative m, Monad m) => MonadProject m where
+  -- | A data type representing an entry in the project.
+  type Entry m
+
+  -- | Prints out a warning message.
+  projectWarn :: String -> m ()
+
+  -- | Prints out an error message, then aborts execution.
+  projectDie :: String -> m a
+
+  -- | Prints out a summary message.
+  printSummary :: String -> m ()
+
+  -- | Prints out notification of a file action.
+  printFileAction :: String -> m ()
+
+  -- | Returns the project's configuration.
+  getConfig :: m Config
+
+  -- | If the program's current path is within the project, then this returns
+  -- the corresponding 'ProjectPath', calling 'projectDie' otherwise.  The
+  -- argument is a sentence fragment explaing the cause, starting with "because
+  -- ...", "for ...", etc. and not ending in punctuation.
+  getCurrentPathOrDie :: String -> m ProjectPath
+
+  -- | Takes a file path and canonicalizes it.  If this path is below the
+  -- project root then a 'ProjectPath' is returned, otherwise an error message
+  -- is returned.
+  parseRealPath :: FilePath -> m (Either String ProjectPath)
+
+  -- | Converts a 'ProjectPath' to an absolute 'FilePath'.
+  pathRealize :: ProjectPath -> m FilePath
+
+  -- | Converts an 'EntrySpec' into 'ProjectPaths' as follows.  Absolute and
+  -- relative 'EntrySpec's get converted to the single path that they point to,
+  -- __whether or not it exists__.  By-name 'EntrySpec's get converted to the
+  -- list of paths that __actually exist__.
+  entrySpecLookup :: EntrySpec -> m [ProjectPath]
+
+  -- | Checks whether there is an entry at a specific path, and returns it, if
+  -- found.
+  entryAtPath :: ProjectPath -> m (Maybe (Entry m))
+
+  -- | Runs a query over entries in the project.
+  queryEntries :: Query -> m [Entry m]
+
+  -- | Returns all of an entry's hard links.
+  entryHardLinks :: Entry m -> m [ProjectPath]
+
+  -- | Returns all of an entry's soft links.
+  entrySoftLinks :: Entry m -> m [ProjectPath]
+
+  -- | Returns an arbitrary source path for an entry, if it has one.
+  entrySourcePath :: Entry m -> m (Maybe ProjectPath)
+
+  -- | Returns all of the tags associated with an entry.
+  entryTags :: Entry m -> m [Tag]
+
+  -- | Returns all tags.
+  tagList :: m (Set Tag)
+
+  -- | Returns all tags that match a specification.
+  tagLookup :: EntrySpec -> m [Tag]
+
+  -- | @'tagLookup1' caller spec@ calls @'tagLookup' spec@.  If 'tagLookup'
+  -- returns a single tag, then so does 'tagLookup1'.  If 'tagLookup' returns
+  -- zero or multiple entries, then 'tagLookup1' calls 'projectDie' with an
+  -- error message that includes @caller@.
+  tagLookup1 :: String -> EntrySpec -> m Tag
+  tagLookup1 caller spec = do
+    tags <- tagLookup spec
+    case tags of
+      [tag] -> return tag
+      _ -> do
+        let count = length tags
+        projectDie $ concat
+          ["tagLookup1 via ", caller, ": ", show spec,
+           " should match one tag but matched ",
+           show count, ": ", show (take 10 tags),
+           if count > 10 then ", ..." else ""]
+
+  -- | Creates a tag, if it doesn't exist.  Returns the tag, and whether the tag
+  -- was newly created.  By-name specifications are not allowed here.
+  tagCreate :: EntrySpec -> m (Tag, Bool)
+
+  -- | Associates each entry with each tag given.
+  tagAdd :: [Entry m] -> [Tag] -> m ()
+
+  -- | Associates an entry with a single tag.  If given a @Just String@, the string will be
+  -- used for the file name of the soft link created (but if the entry already
+  -- has this tag, then a link already exists and this link won't be created).
+  tagAdd1 :: Entry m -> Tag -> Maybe String -> m ()
+
+  -- | Disassociates each entry from each tag given.
+  tagRemove :: [Entry m] -> [Tag] -> m ()
+
+instance MonadProject m => MonadProject (ParsecT s u m) where
+  type Entry (ParsecT s u m) = Entry m
+
+  projectWarn = lift . projectWarn
+  projectDie = lift . projectDie
+  printSummary = lift . printSummary
+  printFileAction = lift . printFileAction
+  getConfig = lift getConfig
+  getCurrentPathOrDie = lift . getCurrentPathOrDie
+  parseRealPath = lift . parseRealPath
+  pathRealize = lift . pathRealize
+  entrySpecLookup = lift . entrySpecLookup
+  entryAtPath = lift . entryAtPath
+  queryEntries = lift . queryEntries
+  entryHardLinks = lift . entryHardLinks
+  entrySoftLinks = lift . entrySoftLinks
+  entrySourcePath = lift . entrySourcePath
+  entryTags = lift . entryTags
+  tagList = lift tagList
+  tagLookup = lift . tagLookup
+  tagLookup1 = (lift .) . tagLookup1
+  tagCreate = lift . tagCreate
+  tagAdd = (lift .) . tagAdd
+  tagAdd1 = ((lift .) .) . tagAdd1
+  tagRemove = (lift .) . tagRemove
+
+dumpProjectContents :: (MonadIO m, MonadProject m) => m ()
+dumpProjectContents = do
+  liftIO $ putStrLn "<<< Project contents dump"
+  entries <- queryEntries LogicTrue
+  forM_ entries $ \entry -> do
+    liftIO $ putStrLn "- Entry"
+    hardLinks <- entryHardLinks entry
+    softLinks <- entrySoftLinks entry
+    tags <- entryTags entry
+    forM_ hardLinks $ showLink "Hard"
+    forM_ softLinks $ showLink "Soft"
+    forM_ tags $ \tag -> liftIO $ putStrLn $ concat ["  - Tag: ", tagToRelativePath tag]
+  liftIO $ putStrLn ">>> Project contents dump"
+
+  where showLink label projectPath = do
+          let path = projectPathToRelativePath projectPath
+          liftIO $ putStrLn $ concat ["  - ", label, " link: ", show path]
diff --git a/src/Khph/Query/Base.hs b/src/Khph/Query/Base.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Query/Base.hs
@@ -0,0 +1,120 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+-- | Data types for constructing predicates.
+module Khph.Query.Base (
+  Logic (..),
+  ListPredicate (..),
+  Query, Query' (..),
+  StringQuery, StringQuery' (..),
+  LinkQuery, LinkQuery' (..),
+  ProjectPathComponent (..),
+  TreeQuery, TreeQuery' (..),
+  TagQuery,
+  ) where
+
+import Khph.Project.Base
+import Khph.Util
+
+-- | Wraps a query of type @q@ in Boolean logic.
+data Logic q =
+    LogicQuery q
+  | LogicTrue
+  | LogicFalse
+  | LogicNot (Logic q)
+  | LogicAnd [Logic q]
+  | LogicOr [Logic q]
+  deriving (Eq, Show)
+
+-- | Represent a fold of a query @q@ over a list.
+--
+-- TODO Count lt/gt operators?  Useful for e.g. "more than one place tag."
+data ListPredicate q =
+    All q
+    -- ^ All items in the list must match @q@.
+  | All1 q
+    -- ^ All items in the list must match @q@, and the list must be nonempty.
+  | Some q
+    -- ^ Some item in the list must match @q@.
+  | None q
+    -- ^ All items in the list must not match @q@.
+  | Exists
+    -- ^ The list must be nonempty.
+  | DoesNotExist
+    -- ^ The list must be empty.
+  deriving (Eq, Show)
+
+-- | A query on an entry.
+type Query = Logic Query'
+
+data Query' =
+    QueryLink (ListPredicate LinkQuery)
+  | QueryTag (ListPredicate TagQuery)
+  deriving (Eq, Show)
+
+-- | A query on a string.
+type StringQuery = Logic StringQuery'
+
+data StringQuery' =
+    StringEq String
+  | StringContains String
+  | StringStartsWith String
+  | StringEndsWith String
+  deriving (Eq, Show)
+
+-- | A query on one of an entry's links.
+type LinkQuery = Logic LinkQuery'
+
+data LinkQuery' =
+    LinkTypeIs LinkType
+    -- ^ Matches based on whether the link is hard or soft.
+  | LinkMatchesEntrySpec EntrySpec
+    -- ^ Matches based on an 'EntrySpec'.
+  | LinkIsSourcePath
+    -- ^ Matches if the link is at or below one of the project's source
+    -- directories.
+  | LinkStringQuery (Maybe ProjectPathComponent) StringQuery
+    -- ^ Matches if a 'StringQuery' matches the project-relative path's textual
+    -- representation.  'ProjectPathComponent' may be used to select only the
+    -- directory or file name components of the path.
+  | LinkTreeQuery (TreeQuery [String])
+    -- ^ Matches if a 'TreeQuery' matches the link's position in the directory
+    -- tree.
+  deriving (Eq, Show)
+
+data ProjectPathComponent = DirectoryComponent | FileComponent
+                          deriving (Eq, Show)
+
+-- | A query on a position in a tree.  @a@ may be an arbitrary data type, that
+-- must be convertible into a @Eq b => [b]@ for comparison.
+type TreeQuery a = Logic (TreeQuery' a)
+
+data TreeQuery' a =
+    TreeAt a
+    -- ^ The position must be at the exact location given.
+  | TreeAtAbove a
+    -- ^ The position must either at or be an ancestor of the location given.
+  | TreeAbove a
+    -- ^ The position must be an ancestor (not at) the location given.
+  | TreeAtBelow a
+    -- ^ The position must either at or be a child of the location given.
+  | TreeBelow a
+    -- ^ The position must be a child (not at) the location given.
+  deriving (Eq, Show)
+
+-- | A tag query is just a query on the tag's position in the tag hierarchy.
+type TagQuery = TreeQuery Tag
diff --git a/src/Khph/Query/Eval.hs b/src/Khph/Query/Eval.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Query/Eval.hs
@@ -0,0 +1,109 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE CPP #-}
+
+-- | Evaluator for a parsed query.
+module Khph.Query.Eval (queryApply) where
+
+#if !MIN_VERSION_base(4,8,0)
+import Control.Applicative ((<$>), (<*>))
+#endif
+import Data.List (intercalate, isInfixOf, isPrefixOf, isSuffixOf)
+import qualified Data.Set as Set
+import Khph.Config (configSourceDirs)
+import Khph.Project.Base
+import Khph.Project.Monad
+import Khph.Query.Base
+import Khph.Util
+import System.FilePath (pathSeparator)
+
+-- | Evaluates a query for a specific entry, returning whether the query matches
+-- the entry.
+queryApply :: MonadProject m => Query -> Entry m -> m Bool
+queryApply logic entry = logicApply logic $ \query -> case query of
+  QueryLink listPredicate -> do
+    links <- (++) <$>
+             (map (\path -> (path, HardLink)) <$> entryHardLinks entry) <*>
+             (map (\path -> (path, SoftLink)) <$> entrySoftLinks entry)
+    listPredicateApply listPredicate queryLink links
+  QueryTag listPredicate -> do
+    tags <- entryTags entry
+    listPredicateApply listPredicate (\q xs -> queryTree tagToComponents q xs) $
+      map tagToComponents tags
+
+queryLink :: MonadProject m => LinkQuery -> (ProjectPath, LinkType) -> m Bool
+queryLink logic (projectPath, linkType) = logicApply logic $ \query -> case query of
+  LinkTypeIs typ -> return $ typ == linkType
+  LinkMatchesEntrySpec entrySpec -> case entrySpec of
+    EntrySpecAbsolute components ->
+      return $ projectPathToComponents projectPath == components
+    EntrySpecRelative components -> do
+      currentPath <- getCurrentPathOrDie $ "running query " ++ show query
+      return $ projectPath == projectPathAppendComponents currentPath components
+    EntrySpecByName name ->
+      return $ maybeLast (projectPathToComponents projectPath) == Just name
+  LinkIsSourcePath ->
+    any (\sourceDir -> projectPathIsPrefixOf sourceDir projectPath) .
+    Set.toList .
+    configSourceDirs <$>
+    getConfig
+  LinkStringQuery maybeComponent stringQuery ->
+    queryString stringQuery $
+    intercalate [pathSeparator] $
+    (case maybeComponent of
+      Nothing -> id
+      Just DirectoryComponent -> butLast
+      Just FileComponent -> (:[]) . last) $
+    projectPathToComponents projectPath
+  LinkTreeQuery treeQuery ->
+    queryTree id treeQuery $ projectPathToComponents projectPath
+
+queryString :: MonadProject m => StringQuery -> String -> m Bool
+queryString logic xs = logicApply logic $ \query -> return $ case query of
+  StringEq ys -> xs == ys
+  StringContains ys -> ys `isInfixOf` xs  -- TODO This is terribly inefficient.
+  StringStartsWith ys -> ys `isPrefixOf` xs
+  StringEndsWith ys -> ys `isSuffixOf` xs
+
+queryTree :: MonadProject m => Eq b => (a -> [b]) -> TreeQuery a -> [b] -> m Bool
+queryTree resolve logic xs = logicApply logic $ \query -> return $ case query of
+  TreeAt ys' -> xs == resolve ys'
+  TreeAtAbove ys' -> xs `isPrefixOf` resolve ys'
+  TreeAbove ys' -> let ys = resolve ys'
+                   in xs `isPrefixOf` ys && length xs < length ys
+  TreeAtBelow ys' -> resolve ys' `isPrefixOf` xs
+  TreeBelow ys' -> let ys = resolve ys'
+                   in ys `isPrefixOf` xs && length ys < length xs
+
+logicApply :: MonadProject m => Logic q -> (q -> m Bool) -> m Bool
+logicApply logic eval = case logic of
+  LogicQuery query -> eval query
+  LogicTrue -> return True
+  LogicFalse -> return False
+  LogicNot logic' -> not <$> logicApply logic' eval
+  LogicAnd logics -> allM (flip logicApply eval) logics
+  LogicOr logics -> anyM (flip logicApply eval) logics
+
+listPredicateApply :: MonadProject m => ListPredicate q -> (q -> a -> m Bool) -> [a] -> m Bool
+listPredicateApply p f xs = case p of
+  All q -> allM (f q) xs
+  All1 q -> if null xs then return False else allM (f q) xs
+  Some q -> anyM (f q) xs
+  None q -> not <$> anyM (f q) xs
+  Exists -> return $ not $ null xs
+  DoesNotExist -> return $ null xs
diff --git a/src/Khph/Query/Parse.hs b/src/Khph/Query/Parse.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Query/Parse.hs
@@ -0,0 +1,247 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE CPP #-}
+
+-- | Query language parser.
+module Khph.Query.Parse (parseQuery) where
+
+#if !MIN_VERSION_base(4,8,0)
+import Control.Applicative ((<$), (<$>), (<*), (*>))
+#endif
+import Data.Char (toLower)
+import Data.List (intercalate)
+import Khph.Project.Base
+import Khph.Project.Monad
+import Khph.Query.Base
+import Khph.Util
+import Text.Parsec (
+  (<|>),
+  (<?>),
+  ParsecT,
+  anyToken,
+  char,
+  digit,
+  eof,
+  letter,
+  many,
+  many1,
+  noneOf,
+  option,
+  optional,
+  parse,
+  runParserT,
+  sepBy,
+  space,
+  try,
+  )
+import Text.ParserCombinators.Parsec (Parser)
+
+data Term =
+    TWord String
+  | TLiteralString String
+  | TLiteralInteger Integer
+  | TParenL
+  | TParenR
+  deriving (Eq, Show)
+
+-- | Parses a query from a string.  Returns an error message if parsing fails.
+parseQuery :: MonadProject m => String -> m (Either String Query)
+parseQuery str =
+  case parse (terms <* eof) "<terms>" str of
+    Left err -> return $ Left $ show err
+    Right terms -> either (Left . show) return <$>
+                   if null terms
+                   then return $ Right LogicTrue
+                   else runParserT (query <* eof) () "<query>" terms
+
+terms :: Parser [Term]
+terms = term `sepBy` many space
+
+term :: Parser Term
+term =
+  word <|>
+  string <|>
+  integer <|>
+  TParenL <$ char '(' <|>
+  TParenR <$ char ')'
+
+word :: Parser Term
+word = TWord . map toLower <$> many1 letter
+
+string :: Parser Term
+string =
+  TLiteralString <$>
+  (char '"' *> many (stringChar '"') <* char '"' <|>
+   char '\'' *> many (stringChar '\'') <* char '\'')
+  where stringChar :: Char -> Parser Char
+        stringChar delim = do
+          ch <- noneOf [delim]
+          case ch of
+            '\\' -> do
+              ch2 <- anyToken
+              if ch2 == delim
+                then return delim
+                else case ch2 of
+                  '\\' -> return '\\'
+                  '0' -> return '\0'
+                  'n' -> return '\n'
+                  'r' -> return '\r'
+                  't' -> return '\t'
+                  'v' -> return '\v'
+                  _ -> fail $ concat
+                       ["Unknown escape sequence \\", [ch2], " in khph string."]
+            _ -> return ch
+
+integer :: Parser Term
+integer =
+  TLiteralInteger <$>
+  ((char '-' *> (negate . read <$> digits)) <|>
+   read <$> digits)
+  where digits = many1 digit
+
+type TermParserT = ParsecT [Term] ()
+
+logic :: MonadProject m => TermParserT m q -> TermParserT m (Logic q)
+logic q = disjunction q
+
+disjunction :: MonadProject m => TermParserT m q -> TermParserT m (Logic q)
+disjunction q =
+  (\ls -> case ls of
+     [l] -> l
+     _ -> LogicOr ls) <$>
+  conjunction q `mySepBy1` w "or"
+
+conjunction :: MonadProject m => TermParserT m q -> TermParserT m (Logic q)
+conjunction q =
+  (\ls -> case ls of
+     [l] -> l
+     _ -> LogicAnd ls) <$>
+  negation q `mySepBy1` w "and"
+
+negation :: MonadProject m => TermParserT m q -> TermParserT m (Logic q)
+negation q =
+  w "not" *> (LogicNot <$> negation q) <|>
+  logicQuery q
+
+logicQuery :: MonadProject m => TermParserT m q -> TermParserT m (Logic q)
+logicQuery q =
+  pl *> logic q <* pr <|>
+  LogicTrue <$ w "true" <|>
+  LogicFalse <$ w "false" <|>
+  LogicQuery <$> q
+
+listPredicate :: MonadProject m
+              => TermParserT m ()
+              -> TermParserT m a
+              -> TermParserT m (ListPredicate a)
+listPredicate word subparser =
+  try (w "all" *> word *> (All <$> subparser)) <|>
+  try (w "all1" *> word *> (All1 <$> subparser)) <|>
+  try (optional (w "some") *> word *> (option Exists $ Some <$> subparser)) <|>
+  try (w "no" *> word *> (option DoesNotExist $ None <$> subparser))
+
+query :: MonadProject m => TermParserT m Query
+query =
+  logic $
+  QueryLink <$> listPredicate (w "link" <|> w "links" <|>
+                               w "path" <|> w "paths")
+                              linkQuery <|>
+  QueryTag <$> listPredicate (w "tag" <|> w "tags") tagQuery
+
+stringQuery :: MonadProject m => TermParserT m StringQuery
+stringQuery =
+  logic $
+  StringEq <$> (w "eq" *> stringTerm) <|>
+  StringContains <$> ((w "contains" <|> w "contain") *> stringTerm) <|>
+  StringStartsWith <$> ((w "starts" <|> w "start") *> w "with" *> stringTerm) <|>
+  StringEndsWith <$> ((w "ends" <|> w "end") *> w "with" *> stringTerm)
+
+linkQuery :: MonadProject m => TermParserT m LinkQuery
+linkQuery =
+  logic $
+  try (LinkTypeIs <$> (isAre *> (HardLink <$ w "hard" <|>
+                                 SoftLink <$ w "soft"))) <|>
+  LinkMatchesEntrySpec <$> (w "matches" *> entrySpec) <|>
+  LinkIsSourcePath <$ isAre <* w "source" <|>
+  try (w "file" *> (LinkStringQuery (Just FileComponent) <$> stringQuery) <|>
+       w "directory" *> (LinkStringQuery (Just DirectoryComponent) <$> stringQuery) <|>
+       LinkStringQuery Nothing <$> stringQuery) <|>
+  LinkTreeQuery <$> treeQuery (do spec <- entrySpec
+                                  paths <- entrySpecLookup spec
+                                  let count = length paths
+                                      limit = 10
+                                  case paths of
+                                    [path] -> return $ projectPathToComponents path
+                                    _ -> fail $ concat
+                                         ["The EntrySpec given to a LinkTreeQuery should match ",
+                                          "a single entry, but we found ", show count, ": ",
+                                          intercalate ", " $ map show $ take limit paths,
+                                          if count > limit then ", ..." else ""])
+
+tagQuery :: MonadProject m => TermParserT m TagQuery
+tagQuery = treeQuery $ tagLookup1 "tagQuery" =<< entrySpec
+
+treeQuery :: MonadProject m => TermParserT m a -> TermParserT m (TreeQuery a)
+treeQuery valueParser =
+  logic $
+  (w "at" *> (TreeAt <$> valueParser)) <|>
+  (w "atabove" *> (TreeAtAbove <$> valueParser)) <|>
+  (w "atbelow" *> (TreeAtBelow <$> valueParser)) <|>
+  (w "above" *> (TreeAbove <$> valueParser)) <|>
+  (w "below" *> (TreeBelow <$> valueParser))
+
+entrySpec :: MonadProject m => TermParserT m EntrySpec
+entrySpec = do
+  str <- stringTerm
+  case toEntrySpec str of
+    Left err -> fail $ concat
+                ["Couldn't parse an EntrySpec from ", show str, ": ", err]
+    Right entrySpec -> return entrySpec
+
+stringTerm :: Monad m => TermParserT m String
+stringTerm =
+  try (do t <- anyToken
+          case t of
+            TLiteralString str -> return str
+            _ -> fail "") <?>
+  "string"
+
+w :: Monad m => String -> TermParserT m ()
+w = parserEq . TWord . map toLower
+
+pl :: Monad m => TermParserT m ()
+pl = parserEq TParenL
+
+pr :: Monad m => TermParserT m ()
+pr = parserEq TParenR
+
+isAre :: Monad m => TermParserT m ()
+isAre = w "is" <|> w "are"
+
+-- | Similar to 'sepBy1', @mySepBy1 body separator@ parses a series of @body@s
+-- separated by @separator@.  However, unlike 'sepBy1', this function wraps each
+-- @separator >> mySepBy1 body separator@ recursive call in a 'try', so seeing a
+-- separator but failing to parse a subsequent body doesn't cause the parse to
+-- fail, because the same separator may be used at a higher level in the syntax
+-- tree.
+mySepBy1 :: TermParserT m a -> TermParserT m b -> TermParserT m [a]
+mySepBy1 body separator = do
+  x <- body
+  -- Instead of the next line, sepBy1 uses "xs <- many (separator body)".
+  xs <- try (separator *> mySepBy1 body separator) <|> return []
+  return $ x:xs
diff --git a/src/Khph/Util.hs b/src/Khph/Util.hs
new file mode 100644
--- /dev/null
+++ b/src/Khph/Util.hs
@@ -0,0 +1,153 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+-- | Miscellaneous utilities.
+module Khph.Util (
+  butLast,
+  maybeLast,
+  splitOn,
+  stripTrailingPathSeparators,
+  anyM,
+  allM,
+  warn,
+  die,
+  rightOrDie,
+  splitPath,
+  pathIsAncestor,
+  droppingIOErrors,
+  LinkType (..),
+  FileType (..),
+  getFileType,
+  parserEq,
+  ) where
+
+import Control.Monad.IO.Class (MonadIO, liftIO)
+import Data.List (findIndex, isPrefixOf)
+import System.Exit (exitFailure)
+import System.FilePath (isPathSeparator, normalise, splitDirectories)
+import System.IO (hPrint, hPutStrLn, stderr)
+import System.IO.Error (
+  catchIOError,
+  doesNotExistErrorType,
+  ioeGetErrorType,
+  tryIOError,
+  )
+import System.Posix (
+  getFileStatus,
+  getSymbolicLinkStatus,
+  isDirectory,
+  isRegularFile,
+  isSymbolicLink,
+  )
+import Text.Parsec ((<?>), ParsecT, anyToken, try)
+
+butLast :: [a] -> [a]
+butLast [] = []
+butLast xs = take (length xs - 1) xs
+
+maybeLast :: [a] -> Maybe a
+maybeLast [] = Nothing
+maybeLast (x:[]) = Just x
+maybeLast (_:xs) = maybeLast xs
+
+-- | Splits a list at elements for which a predicate returns true.  The matching
+-- elements themselves are dropped.
+splitWhen :: (a -> Bool) -> [a] -> [[a]]
+splitWhen _ [] = []
+splitWhen f xs = case findIndex f xs of
+  Just index -> let (term, _:rest) = splitAt index xs
+                in term : splitWhen f rest
+  Nothing -> [xs]
+
+-- | Splits a string on a specified character.
+splitOn :: Char -> String -> [String]
+splitOn ch = splitWhen (== ch)
+
+stripTrailingPathSeparators :: FilePath -> FilePath
+stripTrailingPathSeparators "" = ""
+stripTrailingPathSeparators str =
+  if isPathSeparator $ last str
+  then reverse $ dropWhile isPathSeparator $ reverse str
+  else str
+
+anyM :: Monad m => (a -> m Bool) -> [a] -> m Bool
+anyM _ [] = return False
+anyM f (x:xs) = do b <- f x
+                   if b then return True else anyM f xs
+
+allM :: Monad m => (a -> m Bool) -> [a] -> m Bool
+allM _ [] = return True
+allM f (x:xs) = do b <- f x
+                   if b then allM f xs else return False
+
+warn :: MonadIO m => String -> m ()
+warn msg = liftIO $ hPutStrLn stderr $ "khph: Warning: " ++ msg
+
+die :: MonadIO m => String -> m a
+die msg = liftIO $ do
+  hPutStrLn stderr $ "khph: Error: " ++ msg
+  exitFailure
+
+rightOrDie :: MonadIO m => Either String a -> m a
+rightOrDie = either (liftIO . die) return
+
+splitPath :: FilePath -> [String]
+splitPath = splitDirectories . normalise
+
+pathIsAncestor :: FilePath -> FilePath -> Bool
+pathIsAncestor path1 path2 = splitPath path1 `isPrefixOf` splitPath path2
+
+-- | Executes an IO action, calling the handler function if the action succeeds,
+-- and printing the error message to stderr if the action throws an exception.
+droppingIOErrors :: MonadIO m => IO a -> (a -> m ()) -> m ()
+droppingIOErrors action onSuccess = do
+  result <- liftIO $ tryIOError action
+  case result of
+    Left err -> liftIO $ hPrint stderr err
+    Right x -> onSuccess x
+
+data LinkType = HardLink | SoftLink
+              deriving (Eq, Show)
+
+data FileType =
+    Nonexistant
+  | File
+  | Directory
+  | SymlinkTo FileType
+  | Other
+  deriving (Eq, Show)
+
+getFileType :: FilePath -> IO FileType
+getFileType = query getSymbolicLinkStatus
+  where query f path = flip catchIOError handler $ do
+          stat <- f path
+          case undefined of
+            _ | isRegularFile stat -> return File
+            _ | isDirectory stat -> return Directory
+            _ | isSymbolicLink stat -> fmap SymlinkTo $ query getFileStatus path
+            _ -> return Other
+
+        handler e =
+          if ioeGetErrorType e == doesNotExistErrorType
+          then return Nonexistant
+          else ioError e
+
+parserEq :: (Eq a, Show a, Monad m) => a -> ParsecT [a] u m ()
+parserEq t =
+  try (do t' <- anyToken
+          if t == t' then return () else fail "") <?>
+  show t
diff --git a/src/Main.hs b/src/Main.hs
new file mode 100644
--- /dev/null
+++ b/src/Main.hs
@@ -0,0 +1,237 @@
+-- This file is part of khph.
+--
+-- Copyright 2016 Bryan Gardiner <bog@khumba.net>
+--
+-- This program is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU Affero General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU Affero General Public License for more details.
+--
+-- You should have received a copy of the GNU Affero General Public License
+-- along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+{-# LANGUAGE CPP #-}
+
+module Main (main) where
+
+#if !MIN_VERSION_base(4,8,0)
+import Control.Applicative ((<$>))
+#endif
+import Control.Monad ((<=<), forM_, unless)
+import Control.Monad.IO.Class (liftIO)
+import Data.Either (partitionEithers)
+import Data.List (intercalate, isSuffixOf)
+import Data.Maybe (catMaybes, isNothing)
+import qualified Data.Set as Set
+import qualified Khph.Args as Args
+import Khph.Project.Base
+import qualified Khph.Project.Impl as ProjectImpl
+import Khph.Project.Monad
+import Khph.Query.Base
+import Khph.Query.Parse
+import Khph.Util
+import System.Directory (
+  canonicalizePath,
+  getCurrentDirectory,
+  getDirectoryContents,
+  )
+import System.Exit (exitFailure)
+import System.FilePath (
+  (</>),
+  pathSeparator,
+  replaceBaseName,
+  takeBaseName,
+  takeDirectory,
+  takeFileName,
+  )
+import System.IO (hPutStrLn, stderr)
+import System.Posix.Files (getFileStatus, isDirectory, isRegularFile)
+
+main :: IO ()
+main = do
+  flagsResult <- Args.parseFlags
+  case flagsResult of
+    Left err -> do
+      hPutStrLn stderr $ "khph: " ++ err
+      exitFailure
+    Right (commonArgs, maybeRequest) -> do
+      initialDirectory <- canonicalizePath =<< getCurrentDirectory
+
+      -- Find a project file to use.
+      (projectRoot, maybeProjectFile) <- case Args.caProject commonArgs of
+        "" -> do
+          result <- findProjectFile True initialDirectory
+          case result of
+            Nothing -> die "Couldn't find a project."
+            Just path -> return (takeDirectory path, Just $ takeFileName path)
+        pathRaw -> do
+          path <- canonicalizePath pathRaw
+          stat <- getFileStatus path
+          case undefined of
+            _ | isRegularFile stat ->
+              return (takeDirectory path, Just $ takeFileName path)
+            _ | isDirectory stat -> do
+              maybeProjectFile <- findProjectFile False path
+              return (path, maybeProjectFile)
+            _ -> die $ concat
+                 ["--project expects a regular file or directory.  Got ", show path, "."]
+
+      ProjectImpl.run commonArgs projectRoot maybeProjectFile $ do
+        request <- case maybeRequest of
+          Just request -> return request
+          Nothing -> liftIO $ do
+            putStr $ unlines
+              [ "khph: " ++ Args.description
+              , "See --help for more information."
+              ]
+            exitFailure
+
+        case request of
+          Args.Help ->
+            -- Printing the help message is handled by the argument parser.
+            return ()
+
+          Args.List {Args.listQuery = queryStrMaybe} -> do
+            query <- case queryStrMaybe of
+              Nothing -> return LogicTrue
+              Just queryStr -> parseQueryOrDie queryStr
+            printSummary $ "Query: " ++ show query
+
+            entries <- queryEntries query
+            forM_ entries $ \entry -> do
+              hardLinks <- entryHardLinks entry
+              links <- if not $ null hardLinks
+                       then return hardLinks
+                       else entrySoftLinks entry
+              path <- case links of
+                [] -> projectDie $ concat
+                      ["list: Internal error, should have links for ", show entry, " but don't."]
+                link:_ -> return link
+              liftIO . putStrLn =<< pathRealize path
+
+            let entryCount = length entries
+            printSummary $ concat
+              ["Found ", show entryCount, if entryCount == 1 then " entry." else " entries."]
+
+          Args.TagList {Args.tagListSpec = entrySpecStrMaybe} -> do
+            tags <- case entrySpecStrMaybe of
+              Nothing -> Set.toList <$> tagList
+              Just entrySpecStr -> tagLookup =<< parseEntrySpecOrDie entrySpecStr
+            forM_ tags $ liftIO . putStrLn . tagToRelativePath
+
+          Args.TagCreate {Args.tags = tagStrs} ->
+            forM_ tagStrs $ tagCreate <=< parseEntrySpecOrDie
+
+          Args.TagAdd { Args.files = files
+                      , Args.tags = tagStrs
+                      } -> do
+            projectPaths <- parsePathsOrDie files
+            entries <- findEntriesOrDie projectPaths
+            tags <- findTagsOrDie tagStrs
+            tagAdd entries tags
+
+          Args.TagRemove { Args.files = files
+                         , Args.tags = tagStrs
+                         } -> do
+            projectPaths <- parsePathsOrDie files
+            entries <- findEntriesOrDie projectPaths
+            tags <- findTagsOrDie tagStrs
+            tagRemove entries tags
+
+          Args.Realize { Args.tag = tagStr
+                       , Args.query = queryStr
+                       , Args.tagsInName = tagsInName
+                       } -> do
+            -- Parse inputs.
+            entrySpec <- parseEntrySpecOrDie tagStr
+            query <- parseQueryOrDie queryStr
+
+            -- Look up (or create) the tag, and remove the tag's existing
+            -- association with all entries.  If you're realizing a query for
+            -- entries with a tag, you don't want the target tag contributing to
+            -- that!
+            (tag, tagIsNew) <- tagCreate entrySpec
+            unless tagIsNew $ do
+              entriesOld <- queryEntries $ LogicQuery $ QueryTag $ Some $ LogicQuery $ TreeAt tag
+              tagRemove entriesOld [tag]
+
+            entriesNew <- queryEntries query
+            forM_ entriesNew $ \entry -> do
+              etags <- entryTags entry
+              sourcePath <- maybe (projectDie $ concat
+                                   ["realize: ", show entry, " should have a source path."])
+                                  return =<<
+                            entrySourcePath entry
+
+              -- If requested, then we add tags into link file names.
+              let linkFileName = if tagsInName
+                                 then Just $ replaceBaseName targetFileName newBaseName
+                                 else Nothing
+                  -- The following are only used when tagsInName is true.
+                  renderedTags =
+                    map (map (\c -> if c == pathSeparator then '-' else c) .
+                         tagToRelativePath) etags
+                  targetFileName = takeFileName $ projectPathToRelativePath sourcePath
+                  newBaseName = intercalate " " $ takeBaseName targetFileName : renderedTags
+
+              tagAdd1 entry tag linkFileName
+
+            let entryCount = length entriesNew
+            printSummary $ concat
+              ["Found ", show entryCount, if entryCount == 1 then " entry." else " entries."]
+
+          _ -> projectDie "khph: Unimplemented command."
+
+findProjectFile :: Bool -> FilePath -> IO (Maybe FilePath)
+findProjectFile recur startingDirectory = do
+  contents <- getDirectoryContents startingDirectory
+  let projectFiles = filter (".khph" `isSuffixOf`) contents
+  case projectFiles of
+    projectFile:_ -> return $ Just $ startingDirectory </> projectFile
+    [] -> if recur
+          then let parent = takeDirectory startingDirectory
+               in if parent == startingDirectory
+                  then return Nothing
+                  else findProjectFile recur parent
+          else return Nothing
+
+parsePathsOrDie :: MonadProject m => [FilePath] -> m [ProjectPath]
+parsePathsOrDie pathStrs = do
+  (errors, projectPaths) <- partitionEithers <$> mapM parseRealPath pathStrs
+  if null errors
+    then return projectPaths
+    else projectDie $ concat $
+         "parsePathsOrDie: Couldn't parse some paths: " : map ("\n- " ++) errors
+
+findEntriesOrDie :: MonadProject m => [ProjectPath] -> m [Entry m]
+findEntriesOrDie projectPaths = do
+  entriesResult <- mapM (\p -> (,) p <$> entryAtPath p) projectPaths
+  case filter (isNothing . snd) entriesResult of
+    [] -> return $ catMaybes $ map snd entriesResult
+    xs -> projectDie $ concat $
+          "findEntriesOrDie: Couldn't find some entries: " :
+          map (("\n- " ++) . projectPathToRelativePath . fst) xs
+
+findTagsOrDie :: MonadProject m => [String] -> m [Tag]
+findTagsOrDie = mapM $ tagLookup1 "main" <=< parseEntrySpecOrDie
+
+parseEntrySpecOrDie :: MonadProject m => String -> m EntrySpec
+parseEntrySpecOrDie specStr = case toEntrySpec specStr of
+  Left err ->
+    projectDie $ concat
+    ["parseEntrySpecOrDie: Couldn't parse EntrySpec from ", show specStr, ": ", err]
+  Right entrySpec -> return entrySpec
+
+parseQueryOrDie :: MonadProject m => String -> m Query
+parseQueryOrDie queryStr = do
+  queryResult <- parseQuery queryStr
+  case queryResult of
+    Left err ->
+      projectDie $ concat
+      ["parseQueryOrDie: Error parsing query from ", show queryStr, ": ", err]
+    Right query -> return query
