It looks that during .lhs -> .hs switch the comments were not updated. Grepping for ".lhs" reveals 117 lines where .lhs files are referenced:

basicTypes/OccName.hs:154:-- see also: Note [Data Constructor Naming] in DataCon.lhs
basicTypes/BasicTypes.hs:447:-- instance. See Note [Safe Haskell isSafeOverlap] (in `InstEnv.lhs`) for a
basicTypes/BasicTypes.hs:874:      Note [Expanding variables] in Rules.lhs.
basicTypes/Id.hs:579:-- See Note [Specialisations and RULES in IdInfo] in IdInfo.lhs
basicTypes/Id.hs:689:        -- Another good example is in fill_in in PrelPack.lhs.  We should be able to
basicTypes/DataCon.hs:407:                -- See also Note [Data-con worker strictness] in MkId.lhs
basicTypes/MkId.hs:1194:   See DsUtils.lhs Note [Desugaring seq (1)] and (2) and (3)
basicTypes/Var.hs:340:-- Ids, because Id.lhs uses 'mkGlobalId' etc with different types
basicTypes/IdInfo.hs:423:-- CafInfo is used to build Static Reference Tables (see simplStg/SRT.lhs).
cmm/CmmBuildInfoTables.hs:201:-- Adapted from simpleStg/SRT.lhs, which expects Id's.
cmm/cmm-notes:98:SMRep.lhs
cmm/cmm-notes:123:CodeGen.lhs
cmm/cmm-notes:124:CgBindery.lhs
cmm/cmm-notes:126:CgCase.lhs
cmm/cmm-notes:127:CgClosure.lhs
cmm/cmm-notes:128:CgCon.lhs
cmm/cmm-notes:129:CgExpr.lhs
cmm/cmm-notes:130:CgLetNoEscape.lhs
cmm/cmm-notes:132:CgHeapery.lhs
cmm/cmm-notes:135:CgMonad.lhs
cmm/cmm-notes:139:CgStackery.lhs
cmm/cmm-notes:140:CgTailCall.lhs
cmm/cmm-notes:143:ClosureInfo.lhs
codeGen/StgCmmBind.hs:744:        -- CgConTbls.lhs with a description generated from the data constructor
codeGen/StgCmmExpr.hs:704:-- stgSyn/CoreToStg.lhs). Consider this:
coreSyn/CorePrep.hs:111:9.  Replace (lazy e) by e.  See Note [lazyId magic] in MkId.lhs
coreSyn/CoreUtils.hs:803:~~~~~~~~~~~~~~~~~~   in CoreUnfold.lhs
coreSyn/CoreSyn.hs:245:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
coreSyn/CoreSyn.hs:268:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
coreSyn/CoreSyn.hs:274:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
coreSyn/CoreSyn.hs:289:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
coreSyn/CoreSyn.hs:438:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
coreSyn/CoreSyn.hs:764:                -- See Note [Extra args in rule matching] in Rules.lhs
coreSyn/CoreSyn.hs:921:                       -- (see MkId.lhs, calls to mkCompulsoryUnfolding).
coreSyn/CoreSyn.hs:1100:--   See Note [Expanding variables] in Rules.lhs
coreSyn/CoreSyn.hs:1256:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
coreSyn/CoreSyn.hs:1445:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
coreSyn/CoreArity.hs:612:See Note [Dictionary-like types] in TcType.lhs for why we use
coreSyn/CoreFVs.hs:294:            -- See Note [Finding rule RHS free vars] in OccAnal.lhs
coreSyn/CoreFVs.hs:393:-- This actually happened in the defn of errorIO in IOBase.lhs:
deSugar/DsExpr.hs:479:        T (recConErr t1 "M.lhs/230/op1")
deSugar/DsExpr.hs:481:          (recConErr t1 "M.lhs/230/op3")
deSugar/DsExpr.hs:486:        M.lhs, line 230: missing field op1 was evaluated
deSugar/DsExpr.hs:531:          other        -> recUpdError "M.lhs/230"
deSugar/DsForeign.hs:673:   -- codeGen/CodeGen.lhs; however, stginit functions have a negative impact
deSugar/Check.hs:56: @Match.lhs@ to generate code)
deSugar/Check.hs:631:tidy_eqn does more or less the same thing as @tidy@ in @Match.lhs@;
ghci/ByteCodeGen.hs:1157:             -- the DataCon.  See DataCon.lhs for details.
ghci/Linker.hs:1109:            -- compiler/ghci/Linker.lhs + rts/Linker.c link the
ghc.mk:243:#		Generate supporting stuff for prelude/PrimOp.lhs
hsSyn/HsDecls.hs:371:   (DefMeth is defined in Class.lhs)
hsSyn/Convert.hs:884:        -- Convert.lhs, hence panic
iface/IfaceType.hs:467:-- See equivalent function in TypeRep.lhs
iface/LoadIface.hs:197:                -- compiling Float.lhs, which mentions Float of course
main/HscMain.hs:356:            --   - filter out the .hs/.lhs source filename if we have one
main/TidyPgm.hs:1266:    -- split (see Note [Worker-wrapper for bottoming functions] in WorkWrap.lhs
main/GHC.hs:1182:{- ToDo: Move the primary logic here to compiler/main/Packages.lhs
main/DriverPhases.hs:52:   literate pre-processor | .lhs          | -             | -
main/Finder.hs:307:-- not a reexport (this invariant is upheld by @Packages.lhs@) and (2)
main/DriverPipeline.hs:827:       -- libraries/hpc/tests/function/subdir/tough2.lhs
main/DriverPipeline.hs:1687:          -- compiler/nativeGen/AsmCodeGen.lhs for another instance
main/HscTypes.hs:1066:                                         -- See Note [Overall plumbing for rules] in Rules.lhs
main/HscTypes.hs:2704:This stuff is in here, rather than (say) in Linker.lhs, because the Linker.lhs
nativeGen/PPC/CodeGen.hs:893:      nonvolatile registers differs (see MachRegs.lhs).
nativeGen/PIC.hs:748:-- (See PprMach.lhs)
nativeGen/RegAlloc/Graph/TrivColorable.hs:73:32% of total compile time and 42% of total alloc when compiling SHA1.lhs from darcs.
nativeGen/RegAlloc/Graph/TrivColorable.hs:81:the most efficient variant tried. Benchmark compiling 10-times SHA1.lhs follows.
parser/cutils.h:9:// Out-of-line string functions, see PrimPacked.lhs
prelude/TysPrim.hs:333:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
prelude/TysPrim.hs:531:defined in \tr{TysWiredIn.lhs}, not here.
prelude/PrimOp.hs:188:is done with plain ccalls now (see PrelNumExtra.lhs).
prelude/PrimOp.hs:486:@primOpIsCheap@, as used in \tr{SimplUtils.lhs}.  For now (HACK
prelude/PrelRules.hs:1006:  -- See Note [Integer division constant folding] in libraries/base/GHC/Real.lhs
prelude/PrelRules.hs:1137:-- See Note [magicDictId magic] in `basicTypes/MkId.lhs`
rename/RnPat.hs:238:    --       before going on to the RHSes (see RnSource.lhs).
rename/RnEnv.hs:1374:                -- See Note [Binders in Template Haskell] in Convert.lhs
rename/RnExpr.hs:316:wired-in. See the Note about the NameSorts in Name.lhs.
simplCore/SimplUtils.hs:1491:                  poly_id   = transferPolyIdInfo var tvs_here $ -- Note [transferPolyIdInfo] in Id.lhs
simplCore/SimplUtils.hs:1624:was like this (base/Foreign/C/Err/Error.lhs):
simplCore/OccurAnal.hs:286:recursive functions] in Simplify.lhs
simplCore/FloatIn.hs:86:SetLevels.lhs module, which tags things with their level numbers.
simplCore/SetLevels.hs:830:       -- See Note [Computing one-shot info] in Demand.lhs
simplCore/SetLevels.hs:1053:    mk_poly_bndr bndr uniq = transferPolyIdInfo bndr abs_vars $         -- Note [transferPolyIdInfo] in Id.lhs
simplCore/SimplCore.hs:299:                        -- Reason: see Note [Shadowing] in SpecConstr.lhs
simplCore/SimplCore.hs:634:                -- See Note [Overall plumbing for rules] in Rules.lhs
simplCore/Simplify.hs:55:the simplifier is in SimplCore.lhs.
simplCore/Simplify.hs:2161:        -- See Note [Data-con worker strictness] in MkId.lhs
simplCore/Simplify.hs:2630:The Ord instance of Maybe in PrelMaybe.lhs, for example, took several extra
simplStg/UnariseStg.hs:66:  where -- See Note [Nullary unboxed tuple] in Type.lhs
specialise/SpecConstr.hs:1839:        -- See Note [Matching lets] in Rule.lhs
specialise/SpecConstr.hs:1845:{- Disabled; see Note [Matching cases] in Rule.lhs
stgSyn/CoreToStg.hs:92:-- constructing SRTs (see SRT.lhs).
stgSyn/CoreToStg.hs:444:        -- See Note [Nullary unboxed tuple] in Type.lhs
stranal/DmdAnal.hs:1089:-- See Note [Trimming a demand to a type] in Demand.lhs
typecheck/TcForeign.hs:137:                   -- See Note [Expanding newtypes] in TyCon.lhs
typecheck/FamInst.hs:327:-- in FamInstEnv.lhs
typecheck/TcExpr.hs:1321:Note [Converting strings] in Convert.lhs
typecheck/TcType.hs:259:It's knot-tied back to Var.lhs.  There is no reason in principle
typecheck/TcType.hs:260:why Var.lhs shouldn't actually have the definition, but it "belongs" here.
typecheck/TcEvidence.hs:138:                  [TcCoercion]            -- See [CoAxiom Index] in Coercion.lhs
typecheck/TcPat.hs:679:As explained by [Wrappers for data instance tycons] in MkIds.lhs, the
typecheck/TcInteract.hs:1524:To achieve this required some refactoring of FunDeps.lhs (nicer
typecheck/TcTyClsDecls.hs:1490:    -- See Note [GADT record selectors] in MkId.lhs
types/Kind.hs:218:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/Kind.hs:234:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/CoAxiom.hs:231:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/TyCon.hs:162:See also Note [Wrappers for data instance tycons] in MkId.lhs
types/TyCon.hs:349:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/TypeRep.hs:98:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/Coercion.hs:126:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/Coercion.hs:203:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/Coercion.hs:945:-- of Coercion and the Note [Refl invariant] in types/TypeRep.lhs.
types/Type.hs:606:interfaces.  Notably this plays a role in tcTySigs in TcBinds.lhs.
types/Type.hs:819:-- See Note [GHC Formalism] in coreSyn/CoreLint.lhs
types/Type.hs:1324:-- See Note [Kind Constraint and kind *] in Kinds.lhs
types/Unify.hs:235:-- thing to do.  C.f. Note [Matching variable types] in Rules.lhs
utils/Binary.hs:476:-- yes, we need Binary Integer and Binary Rational in basicTypes/Literal.lhs